rs462437

chr5-2491471-A-Cchr5-2491471-A-Gchr5-2491471-A-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 0.927 in 97,274 control chromosomes in the GnomAD database, including 42,366 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 0.93 (42366 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.83

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 (NFE) allele frequency at 95% confidence interval = 0.956 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: 0.927 AC: 90184 AN: 97242 Hom.: 42369 Cov.: 22

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.927 AC: 90192 AN: 97274 Hom.: 42366 Cov.: 22 AF XY: 0.925 AC XY: 44007 AN XY: 47596

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.941

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.13
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs462437; hg19: chr5-2491585;