rs462437

Variant names:

• chr5-2491471-A-C
• rs462437

Your query was ambiguous. Multiple possible variants found:

• chr5-2491471-A-C
• chr5-2491471-A-G
• chr5-2491471-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.876 AC: 17498 AN: 19970

American (AMR) AF: 0.953 AC: 9743 AN: 10224

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 2285 AN: 2390

East Asian (EAS) AF: 0.659 AC: 1853 AN: 2810

South Asian (SAS) AF: 0.948 AC: 3143 AN: 3316

European-Finnish (FIN) AF: 0.873 AC: 6719 AN: 7698

Middle Eastern (MID) AF: 0.964 AC: 185 AN: 192

European-Non Finnish (NFE) AF: 0.963 AC: 46826 AN: 48630

Other (OTH) AF: 0.941 AC: 1300 AN: 1382

Alfa AF: 0.00 Hom.: 5992

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
PhyloP100		-5.8

Splicing

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

Other links and lift over

dbSNP: rs462437; hg19: chr5-2491585;