rs11691730

chr2-102944668-G-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM182	ENST00000640575.2	c.470-20986G>A		intron_variant		5

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;