2-21191270-T-C

Variant names:

• chr2-21191270-T-C
• rs503662

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 0.643 in 152,008 control chromosomes in the GnomAD database, including 34,365 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 0.64 (34365 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 18 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 = 0.97 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: 0.644 AC: 97766 AN: 151890 Hom.: 34359 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.643 AC: 97797 AN: 152008 Hom.: 34365 Cov.: 31 AF XY: 0.649 AC XY: 48235 AN XY: 74302

African (AFR) AF: 0.343 AC: 14206 AN: 41426

American (AMR) AF: 0.748 AC: 11434 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2197 AN: 3468

East Asian (EAS) AF: 0.993 AC: 5132 AN: 5168

South Asian (SAS) AF: 0.811 AC: 3905 AN: 4814

European-Finnish (FIN) AF: 0.738 AC: 7790 AN: 10556

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50707 AN: 67972

Other (OTH) AF: 0.658 AC: 1389 AN: 2110

Alfa AF: 0.708 Hom.: 53402

Bravo AF: 0.631

Asia WGS AF: 0.882 AC: 3065 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	7.8
DANN	Benign	0.80
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs503662; hg19: chr2-21414142;