chr2-21047682-A-C

Variant names:

• chr2-21047682-A-C
• rs585967

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 0.817 in 152,212 control chromosomes in the GnomAD database, including 51,304 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 0.82 (51304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.817 AC: 124333 AN: 152094 Hom.: 51261 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.817 AC: 124430 AN: 152212 Hom.: 51304 Cov.: 32 AF XY: 0.819 AC XY: 60980 AN XY: 74424

African (AFR) AF: 0.720 AC: 29884 AN: 41504

American (AMR) AF: 0.853 AC: 13055 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2286 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5156 AN: 5174

South Asian (SAS) AF: 0.873 AC: 4210 AN: 4824

European-Finnish (FIN) AF: 0.857 AC: 9088 AN: 10604

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57967 AN: 68014

Other (OTH) AF: 0.814 AC: 1723 AN: 2116

Alfa AF: 0.831 Hom.: 64554

Bravo AF: 0.812

Asia WGS AF: 0.935 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.70
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs585967; hg19: chr2-21270554;