Variant 2-102764375-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_144632.5(TMEM182):c.279G>A(p.Pro93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 1,613,684 control chromosomes in the GnomAD database, including 126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0073 ( 26 hom., cov: 32)

Exomes 𝑓: 0.0069 ( 100 hom. )

Consequence

TMEM182
NM_144632.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0770

Variant links:

Genes affected

TMEM182 (HGNC:26391): (transmembrane protein 182) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM182 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=-0.51).

BP6

Variant 2-102764375-G-A is Benign according to our data. Variant chr2-102764375-G-A is described in ClinVar as [Benign]. Clinvar id is 710195.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.077 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 26 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM182	NM_144632.5 linkuse as main transcript	c.279G>A	p.Pro93=	synonymous_variant	3/5	ENST00000412401.3	NP_653233.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM182	ENST00000412401.3 linkuse as main transcript	c.279G>A	p.Pro93=	synonymous_variant	3/5	1	NM_144632.5	ENSP00000394178	P1	Q6ZP80-1

Frequencies

GnomAD3 genomes

AF:

0.00733

AC:

1114

AN:

151978

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000459

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0529

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00721

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00830

AC:

2084

AN:

251188

Hom.:

AF XY:

0.00802

AC XY:

1089

AN XY:

135754

show subpopulations

Gnomad AFR exome

AF:

0.000861

Gnomad AMR exome

AF:

0.000839

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0508

Gnomad NFE exome

AF:

0.00766

Gnomad OTH exome

AF:

0.00962

GnomAD4 exome

AF:

0.00690

AC:

10084

AN:

1461588

Hom.:

100

Cov.:

AF XY:

0.00674

AC XY:

4904

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.000805

Gnomad4 ASJ exome

AF:

0.00119

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.0534

Gnomad4 NFE exome

AF:

0.00611

Gnomad4 OTH exome

AF:

0.00573

GnomAD4 genome

AF:

0.00732

AC:

1114

AN:

152096

Hom.:

Cov.:

AF XY:

0.00864

AC XY:

642

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.00116

Gnomad4 AMR

AF:

0.000458

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0529

Gnomad4 NFE

AF:

0.00721

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00589

Hom.:

Bravo

AF:

0.00312

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00415

EpiControl

AF:

0.00415

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 27, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

5.9

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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