NM_033056.4:c.3276T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong

The NM_033056.4(PCDH15):c.3276T>C(p.Asn1092Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,461,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000089 ( 0 hom. )

Consequence

PCDH15
NM_033056.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0870

Publications

0 publications found

Variant links:

Genes affected

PCDH15 (HGNC:14674): (protocadherin related 15) This gene is a member of the cadherin superfamily. Family members encode integral membrane proteins that mediate calcium-dependent cell-cell adhesion. It plays an essential role in maintenance of normal retinal and cochlear function. Mutations in this gene result in hearing loss and Usher Syndrome Type IF (USH1F). Extensive alternative splicing resulting in multiple isoforms has been observed in the mouse ortholog. Similar alternatively spliced transcripts are inferred to occur in human, and additional variants are likely to occur. [provided by RefSeq, Dec 2008]

PCDH15 Gene-Disease associations (from GenCC):

autosomal recessive nonsyndromic hearing loss 23
Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), PanelApp Australia
Usher syndrome type 1
Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
Usher syndrome type 1F
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia
hearing loss, autosomal recessive
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
nonsyndromic genetic hearing loss
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

PCDH15 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 10-53938912-A-G is Benign according to our data. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-53938912-A-G is described in CliVar as Likely_benign. Clinvar id is 506095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH15	NM_033056.4 link	c.3276T>C	p.Asn1092Asn	synonymous_variant	Exon 25 of 33	ENST00000320301.11	NP_149045.3	Q96QU1-1
PCDH15	NM_001384140.1 link	c.3276T>C	p.Asn1092Asn	synonymous_variant	Exon 25 of 38	ENST00000644397.2	NP_001371069.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH15	ENST00000320301.11 link	c.3276T>C	p.Asn1092Asn	synonymous_variant	Exon 25 of 33	1	NM_033056.4	ENSP00000322604.6		Q96QU1-1
PCDH15	ENST00000644397.2 link	c.3276T>C	p.Asn1092Asn	synonymous_variant	Exon 25 of 38		NM_001384140.1	ENSP00000495195.1		A0A2R8Y6C0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000796

AC:

AN:

251130

AF XY:

0.0000147

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000176

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000890

AC:

AN:

1461054

Hom.:

Cov.:

AF XY:

0.0000165

AC XY:

AN XY:

726872

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33456

American (AMR)

AF:

0.00

AC:

AN:

44702

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26118

East Asian (EAS)

AF:

0.00

AC:

AN:

39666

South Asian (SAS)

AF:

0.00

AC:

AN:

86242

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53370

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.0000117

AC:

AN:

1111366

Other (OTH)

AF:

0.00

AC:

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.000111

Hom.:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Sep 14, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

p.Asn1092Asn in exon 25 of PCDH15: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 2/111456 Europe an chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadin stitute.org/; dbSNP rs772160626). -

not provided

Benign:1

May 23, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.2

(source)

DANN

Benign

0.39

PhyloP100

-0.087

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over