Variant 17-81232361-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001363764.2(TEPSIN):c.684C>T(p.Pro228Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,535,450 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0023 ( 6 hom. )

Consequence

TEPSIN
NM_001363764.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.20

Variant links:

Genes affected

TEPSIN (HGNC:26458): (TEPSIN adaptor related protein complex 4 accessory protein) Located in coated vesicle membrane; nucleus; and trans-Golgi network membrane. Is extrinsic component of organelle membrane. Colocalizes with AP-4 adaptor complex. [provided by Alliance of Genome Resources, Apr 2022]

TEPSIN links:

TEPSIN (HGNC:):

TEPSIN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 17-81232361-G-A is Benign according to our data. Variant chr17-81232361-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648445.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.2 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEPSIN	NM_001363764.2 linkuse as main transcript	c.684C>T	p.Pro228Pro	synonymous_variant	8/13	ENST00000637944.2	NP_001350693.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEPSIN	ENST00000637944.2 linkuse as main transcript	c.684C>T	p.Pro228Pro	synonymous_variant	8/13	5	NM_001363764.2	ENSP00000490393.1		A0A1B0GV70

Frequencies

GnomAD3 genomes

AF:

0.00230

AC:

350

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000555

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00229

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00146

AC:

196

AN:

134306

Hom.:

AF XY:

0.00145

AC XY:

106

AN XY:

73126

show subpopulations

Gnomad AFR exome

AF:

0.000931

Gnomad AMR exome

AF:

0.000205

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000134

Gnomad FIN exome

AF:

0.0108

Gnomad NFE exome

AF:

0.00228

Gnomad OTH exome

AF:

0.000970

GnomAD4 exome

AF:

0.00226

AC:

3127

AN:

1383136

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

1510

AN XY:

682424

show subpopulations

Gnomad4 AFR exome

AF:

0.000601

Gnomad4 AMR exome

AF:

0.000196

Gnomad4 ASJ exome

AF:

0.0000398

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000758

Gnomad4 FIN exome

AF:

0.0115

Gnomad4 NFE exome

AF:

0.00240

Gnomad4 OTH exome

AF:

0.00190

GnomAD4 genome

AF:

0.00230

AC:

350

AN:

152314

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

189

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.000553

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0122

Gnomad4 NFE

AF:

0.00229

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00240

Hom.:

Bravo

AF:

0.00144

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2022

TEPSIN: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.83

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over