chr2-102944668-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM182	ENST00000640575.2	TSL:5	c.470-20986G>A		intron	N/A	ENSP00000492657.2	A0A1W2PS41

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

African (AFR) AF: 0.367 AC: 15216 AN: 41462

American (AMR) AF: 0.205 AC: 3126 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1408 AN: 5132

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4832

European-Finnish (FIN) AF: 0.119 AC: 1261 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9593 AN: 67986

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.175 Hom.: 7761

Bravo AF: 0.232

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.24
PhyloP100		0.047

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11691730;

hg19: chr2-103561126;