rs2582660

chr5-16270490-C-Achr5-16270490-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/exons	MANE	UniProt

Ensembl

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