rs11691730

Variant names:

• chr2-102944668-G-A
• rs11691730
• ENST00000640575.2:c.470-20986G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000640575.2(TMEM182):​c.470-20986G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,054 control chromosomes in the GnomAD database, including 4,396 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 0.22 (4396 hom., cov: 32)
• Consequence: TMEM182 ENST00000640575.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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.470-20986G>A		intron_variant	Intron 4 of 5	5		ENSP00000492657.2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32925 AN: 151936 Hom.: 4392 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.217 AC: 32962 AN: 152054 Hom.: 4396 Cov.: 32 AF XY: 0.218 AC XY: 16220 AN XY: 74332

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.235

Alfa AF: 0.163 Hom.: 3773

Bravo AF: 0.232

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11691730; hg19: chr2-103561126;