chr2-21191270-T-C

Variant names:

• chr2-21191270-T-C
• rs503662

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.658

Alfa AF: 0.724 Hom.: 37931

Bravo AF: 0.631

Asia WGS AF: 0.882 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs503662; hg19: chr2-21414142;