rs506585

Variant names:

• chr2-21174310-G-A
• rs506585

Your query was ambiguous. Multiple possible variants found:

• chr2-21174310-G-A
• chr2-21174310-G-C
• chr2-21174310-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;