rs9292961

Variant names:

• chr5-20940020-G-A
• rs9292961

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 0.583 in 151,972 control chromosomes in the GnomAD database, including 26,707 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 0.58 (26707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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: 0.583 AC: 88581 AN: 151854 Hom.: 26672 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.583 AC: 88669 AN: 151972 Hom.: 26707 Cov.: 32 AF XY: 0.592 AC XY: 43945 AN XY: 74268

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.610

Alfa AF: 0.520 Hom.: 11939

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292961; hg19: chr5-20940129;