2-102764375-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0770

Genes affected

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

ACMG classification

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 GnomAd at 26 AR gene

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM182	ENST00000412401.3	c.279G>A	p.Pro93=	synonymous_variant	3/5	1	NM_144632.5	P1

Frequencies

GnomAD3 genomes AF: 0.00733 AC: 1114 AN: 151978 Hom.: 26 Cov.: 32

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.: 30 AF XY: 0.00802 AC XY: 1089 AN XY: 135754

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.: 30 AF XY: 0.00674 AC XY: 4904 AN XY: 727106

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.: 26 Cov.: 32 AF XY: 0.00864 AC XY: 642 AN XY: 74316

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.: 3

Bravo AF: 0.00312

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00415

EpiControl AF: 0.00415

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

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

Other links and lift over

dbSNP: rs79354230; hg19: chr2-103380834;