rs506585

chr2-21174310-G-Achr2-21174310-G-Cchr2-21174310-G-T

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 0.766 in 151,980 control chromosomes in the GnomAD database, including 45,094 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 0.77 (45094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.766 AC: 116283 AN: 151862 Hom.: 45054 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.766 AC: 116378 AN: 151980 Hom.: 45094 Cov.: 32 AF XY: 0.768 AC XY: 57014 AN XY: 74284

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.764

Alfa AF: 0.796 Hom.: 100453

Bravo AF: 0.765

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs506585; hg19: chr2-21397182;