2-173387897-T-C

Variant names:

• chr2-173387897-T-C
• rs11679682

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 0.182 in 152,068 control chromosomes in the GnomAD database, including 2,929 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 0.18 (2929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27638 AN: 151950 Hom.: 2932 Cov.: 32

Gnomad AFR AF: 0.0688

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.182 AC: 27632 AN: 152068 Hom.: 2929 Cov.: 32 AF XY: 0.182 AC XY: 13559 AN XY: 74352

African (AFR) AF: 0.0687 AC: 2851 AN: 41492

American (AMR) AF: 0.199 AC: 3043 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.190 AC: 981 AN: 5172

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4812

European-Finnish (FIN) AF: 0.189 AC: 1997 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15676 AN: 67958

Other (OTH) AF: 0.223 AC: 470 AN: 2108

Alfa AF: 0.212 Hom.: 7069

Bravo AF: 0.176

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs11679682; hg19: chr2-174252625;