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GeneBe

16-29812021-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The XM_047435008.1(LOC112268170):c.426A>G(p.Arg142=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.996 in 300,028 control chromosomes in the GnomAD database, including 148,900 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.99 ( 75058 hom., cov: 30)
Exomes 𝑓: 1.0 ( 73842 hom. )

Consequence

LOC112268170
XM_047435008.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.81
Variant links:
Genes affected
MVP-DT (HGNC:56029): (MVP divergent transcript)
PRRT2 (HGNC:30500): (proline rich transmembrane protein 2) This gene encodes a transmembrane protein containing a proline-rich domain in its N-terminal half. Studies in mice suggest that it is predominantly expressed in brain and spinal cord in embryonic and postnatal stages. Mutations in this gene are associated with episodic kinesigenic dyskinesia-1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-29812021-T-C is Benign according to our data. Variant chr16-29812021-T-C is described in ClinVar as [Benign]. Clinvar id is 1267738.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.81 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC112268170XM_047435008.1 linkuse as main transcriptc.426A>G p.Arg142= synonymous_variant 1/2
LOC112268170XM_047435009.1 linkuse as main transcriptc.426A>G p.Arg142= synonymous_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MVP-DTENST00000569039.5 linkuse as main transcriptn.246-1848A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.993
AC:
151019
AN:
152070
Hom.:
75001
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.976
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.997
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.997
GnomAD3 exomes
AF:
0.997
AC:
20955
AN:
21016
Hom.:
10449
AF XY:
0.998
AC XY:
11264
AN XY:
11292
show subpopulations
Gnomad AFR exome
AF:
0.975
Gnomad AMR exome
AF:
0.999
Gnomad ASJ exome
AF:
1.00
Gnomad EAS exome
AF:
1.00
Gnomad SAS exome
AF:
1.00
Gnomad FIN exome
AF:
1.00
Gnomad NFE exome
AF:
1.00
Gnomad OTH exome
AF:
0.999
GnomAD4 exome
AF:
0.999
AC:
147761
AN:
147842
Hom.:
73842
Cov.:
0
AF XY:
1.00
AC XY:
82244
AN XY:
82282
show subpopulations
Gnomad4 AFR exome
AF:
0.974
Gnomad4 AMR exome
AF:
0.999
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
1.00
Gnomad4 OTH exome
AF:
0.999
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.993
AC:
151134
AN:
152186
Hom.:
75058
Cov.:
30
AF XY:
0.993
AC XY:
73848
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.976
Gnomad4 AMR
AF:
0.997
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
1.00
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
1.00
Gnomad4 OTH
AF:
0.997
Alfa
AF:
0.996
Hom.:
9364
Bravo
AF:
0.992
Asia WGS
AF:
0.999
AC:
3469
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxApr 16, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
16
Dann
Benign
0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8054524; hg19: chr16-29823342; API