chr8-115414152-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_014112.5(TRPS1):c.3756C>T(p.Asp1252Asp) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000657 in 152,120 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: 𝑓 0.0000066 ( 0 hom., cov: 32)

Consequence

TRPS1
NM_014112.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.89

Publications

0 publications found

Variant links:

Genes affected

TRPS1 (HGNC:12340): (transcriptional repressor GATA binding 1) This gene encodes a transcription factor that represses GATA-regulated genes and binds to a dynein light chain protein. Binding of the encoded protein to the dynein light chain protein affects binding to GATA consensus sequences and suppresses its transcriptional activity. Defects in this gene are a cause of tricho-rhino-phalangeal syndrome (TRPS) types I-III. [provided by RefSeq, Jul 2008]

TRPS1 Gene-Disease associations (from GenCC):

trichorhinophalangeal syndrome type I
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
trichorhinophalangeal syndrome, type III
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
trichorhinophalangeal syndrome type I or III
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TRPS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 8-115414152-G-A is Benign according to our data. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-115414152-G-A is described in CliVar as Likely_benign. Clinvar id is 2945974.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPS1	NM_014112.5 link	c.3756C>T	p.Asp1252Asp	synonymous_variant	Exon 7 of 7	ENST00000395715.8	NP_054831.2	Q9UHF7-2
TRPS1	NM_001282903.3 link	c.3735C>T	p.Asp1245Asp	synonymous_variant	Exon 7 of 7		NP_001269832.1	Q9UHF7
TRPS1	NM_001282902.3 link	c.3729C>T	p.Asp1243Asp	synonymous_variant	Exon 6 of 6		NP_001269831.1	Q9UHF7-3
TRPS1	NM_001330599.2 link	c.3717C>T	p.Asp1239Asp	synonymous_variant	Exon 6 of 6		NP_001317528.1	Q9UHF7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPS1	ENST00000395715.8 link	c.3756C>T	p.Asp1252Asp	synonymous_variant	Exon 7 of 7	1	NM_014112.5	ENSP00000379065.3		Q9UHF7-2

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152120

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41436

American (AMR)

AF:

0.00

AC:

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68012

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.000224

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Trichorhinophalangeal dysplasia type I;C1860823:Trichorhinophalangeal syndrome, type III

Benign:1

Jan 08, 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

-0.49

CADD

Benign

8.6

(source)

DANN

Benign

0.55

PhyloP100

3.9

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over