2-236149500-T-C

Variant names:

• chr2-236149500-T-C
• rs11687170

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.158 in 151,936 control chromosomes in the GnomAD database, including 2,025 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 0.16 (2025 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23961 AN: 151818 Hom.: 2024 Cov.: 29

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.158 AC: 23972 AN: 151936 Hom.: 2025 Cov.: 29 AF XY: 0.160 AC XY: 11904 AN XY: 74212

African (AFR) AF: 0.128 AC: 5319 AN: 41428

American (AMR) AF: 0.100 AC: 1533 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1097 AN: 5146

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2369 AN: 10536

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11717 AN: 67954

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.159 Hom.: 4909

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.21
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11687170; hg19: chr2-237058144;