rs2423191

Variant names:

• chr20-7312888-C-A
• rs2423191

Your query was ambiguous. Multiple possible variants found:

• chr20-7312888-C-A
• chr20-7312888-C-G
• chr20-7312888-C-T

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 0.407 in 151,894 control chromosomes in the GnomAD database, including 14,033 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 0.41 (14033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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: 0.407 AC: 61827 AN: 151776 Hom.: 14029 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.407 AC: 61836 AN: 151894 Hom.: 14033 Cov.: 32 AF XY: 0.411 AC XY: 30476 AN XY: 74230

African (AFR) AF: 0.194 AC: 8044 AN: 41452

American (AMR) AF: 0.404 AC: 6145 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2857 AN: 5148

South Asian (SAS) AF: 0.466 AC: 2250 AN: 4824

European-Finnish (FIN) AF: 0.559 AC: 5901 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33781 AN: 67932

Other (OTH) AF: 0.396 AC: 835 AN: 2106

Alfa AF: 0.450 Hom.: 7950

Bravo AF: 0.389

Asia WGS AF: 0.449 AC: 1560 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.55
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2423191; hg19: chr20-7293535;