rs585967

Positions:

• chr2-21047682-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;