rs2582660

Variant names:

• chr5-16270490-C-A
• rs2582660

Your query was ambiguous. Multiple possible variants found:

• chr5-16270490-C-A
• chr5-16270490-C-G

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 0.788 in 152,004 control chromosomes in the GnomAD database, including 47,316 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 0.79 (47316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.788 AC: 119681 AN: 151886 Hom.: 47284 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.788 AC: 119768 AN: 152004 Hom.: 47316 Cov.: 32 AF XY: 0.788 AC XY: 58602 AN XY: 74326

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.763

Alfa AF: 0.785 Hom.: 7425

Bravo AF: 0.771

Asia WGS AF: 0.755 AC: 2622 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2582660; hg19: chr5-16270599;