2-173868477-G-C

Variant names:

• chr2-173868477-G-C
• rs16862162

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 0.207 in 152,076 control chromosomes in the GnomAD database, including 4,197 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 0.21 (4197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31449 AN: 151956 Hom.: 4199 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.207 AC: 31450 AN: 152076 Hom.: 4197 Cov.: 32 AF XY: 0.217 AC XY: 16154 AN XY: 74302

African (AFR) AF: 0.111 AC: 4605 AN: 41512

American (AMR) AF: 0.224 AC: 3427 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3472

East Asian (EAS) AF: 0.656 AC: 3391 AN: 5166

South Asian (SAS) AF: 0.467 AC: 2245 AN: 4806

European-Finnish (FIN) AF: 0.304 AC: 3206 AN: 10530

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13110 AN: 67992

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.113 Hom.: 219

Bravo AF: 0.194

Asia WGS AF: 0.530 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.43
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs16862162; hg19: chr2-174733205;