rs464637

Variant names:

• chr5-2340875-G-A
• rs464637

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 0.295 in 150,832 control chromosomes in the GnomAD database, including 7,180 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 0.29 (7180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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: 0.295 AC: 44418 AN: 150712 Hom.: 7160 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.295 AC: 44478 AN: 150832 Hom.: 7180 Cov.: 31 AF XY: 0.301 AC XY: 22114 AN XY: 73584

African (AFR) AF: 0.422 AC: 17332 AN: 41084

American (AMR) AF: 0.312 AC: 4754 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3468

East Asian (EAS) AF: 0.416 AC: 2102 AN: 5048

South Asian (SAS) AF: 0.329 AC: 1569 AN: 4768

European-Finnish (FIN) AF: 0.248 AC: 2529 AN: 10178

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14392 AN: 67766

Other (OTH) AF: 0.290 AC: 609 AN: 2100

Alfa AF: 0.258 Hom.: 686

Bravo AF: 0.306

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.78
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs464637; hg19: chr5-2340989;