rs2922061

Variant names:

• chr5-2585404-A-G
• rs2922061

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 0.581 in 148,034 control chromosomes in the GnomAD database, including 27,502 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 (27502 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 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: 0.581 AC: 85898 AN: 147906 Hom.: 27450 Cov.: 25

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.581 AC: 86004 AN: 148034 Hom.: 27502 Cov.: 25 AF XY: 0.577 AC XY: 41606 AN XY: 72058

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.573

Alfa AF: 0.509 Hom.: 2739

Bravo AF: 0.594

Asia WGS AF: 0.616 AC: 2090 AN: 3392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2922061; hg19: chr5-2585518;