chr2-21047682-A-C

Variant names:

• chr2-21047682-A-C
• rs585967

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 0.817 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.817 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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.814

Alfa AF: 0.816 Hom.: 4705

Bravo AF: 0.812

Asia WGS AF: 0.935 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs585967; hg19: chr2-21270554;