rs13402330

Variant names:

• chr2-102895834-T-A
• rs13402330
• ENST00000640575.2:c.470-69820T>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

LINC01796 (HGNC:52586): (long intergenic non-protein coding RNA 1796)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640575.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01796	NR_135562.1		n.-112A>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM182	ENST00000640575.2	TSL:5	c.470-69820T>A		intron	N/A	ENSP00000492657.2	A0A1W2PS41
	TMEM182	ENST00000639249.1	TSL:5	c.182-37051T>A		intron	N/A	ENSP00000491614.1	A0A1W2PQA2
	LINC01796	ENST00000611915.2	TSL:3	n.-89A>T		upstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.168 AC: 6979 AN: 41496

American (AMR) AF: 0.230 AC: 3507 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3466

East Asian (EAS) AF: 0.175 AC: 908 AN: 5184

South Asian (SAS) AF: 0.193 AC: 930 AN: 4822

European-Finnish (FIN) AF: 0.260 AC: 2753 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13670 AN: 67980

Other (OTH) AF: 0.167 AC: 352 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.55
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs13402330; hg19: chr2-103512292;