rs12052617

Variant names:

• chr2-102862176-G-A
• rs12052617
• ENST00000640575.2:c.469+64176G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000640575.2(TMEM182):​c.469+64176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,220 control chromosomes in the GnomAD database, including 1,818 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1818 hom., cov: 33)
• Consequence: TMEM182 ENST00000640575.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM182	ENST00000640575.2	c.469+64176G>A		intron_variant	Intron 4 of 5	5		ENSP00000492657.2
TMEM182	ENST00000639249.1	c.181+64176G>A		intron_variant	Intron 4 of 4	5		ENSP00000491614.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23126 AN: 152102 Hom.: 1816 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 23154 AN: 152220 Hom.: 1818 Cov.: 33 AF XY: 0.153 AC XY: 11422 AN XY: 74432

African (AFR) AF: 0.170 AC: 7049 AN: 41544

American (AMR) AF: 0.166 AC: 2544 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3466

East Asian (EAS) AF: 0.255 AC: 1323 AN: 5182

South Asian (SAS) AF: 0.181 AC: 875 AN: 4826

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10592

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8996 AN: 68002

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.139 Hom.: 781

Bravo AF: 0.157

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.61
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs12052617; hg19: chr2-103478635;