2-163128427-G-A

Variant names:

• chr2-163128427-G-A
• rs10497231

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 0.196 in 150,888 control chromosomes in the GnomAD database, including 3,062 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 (3062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.196 AC: 29553 AN: 150772 Hom.: 3060 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.196 AC: 29550 AN: 150888 Hom.: 3062 Cov.: 32 AF XY: 0.197 AC XY: 14491 AN XY: 73574

African (AFR) AF: 0.121 AC: 5031 AN: 41434

American (AMR) AF: 0.224 AC: 3377 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 683 AN: 3458

East Asian (EAS) AF: 0.181 AC: 914 AN: 5038

South Asian (SAS) AF: 0.109 AC: 508 AN: 4662

European-Finnish (FIN) AF: 0.233 AC: 2442 AN: 10460

Middle Eastern (MID) AF: 0.226 AC: 57 AN: 252

European-Non Finnish (NFE) AF: 0.236 AC: 15927 AN: 67516

Other (OTH) AF: 0.205 AC: 429 AN: 2090

Alfa AF: 0.213 Hom.: 425

Bravo AF: 0.194

Asia WGS AF: 0.134 AC: 457 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.47
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10497231; hg19: chr2-163984937;