rs13402330

Positions:

• chr2-102895834-T-A
• chr2-102895834-T-C

Variant summary

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

The ENST00000640575.2(TMEM182):​c.470-69820T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,132 control chromosomes in the GnomAD database, including 3,020 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 0.20 (3020 hom., cov: 32)
  • Exomes 𝑓: 0.28 (0 hom.)
• Consequence: TMEM182 ENST00000640575.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM182	ENST00000639249.1	c.182-37051T>A		intron_variant		5		ENSP00000491614
TMEM182	ENST00000640575.2	c.470-69820T>A		intron_variant		5		ENSP00000492657

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29750 AN: 151996 Hom.: 3017 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.278 AC: 5 AN: 18 Hom.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.214

GnomAD4 genome AF: 0.196 AC: 29782 AN: 152114 Hom.: 3020 Cov.: 32 AF XY: 0.198 AC XY: 14734 AN XY: 74348

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.167

Alfa AF: 0.127 Hom.: 215

Bravo AF: 0.190

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13402330; hg19: chr2-103512292;