rs464637

Positions:

• chr5-2340875-G-A

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 0.295 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.290

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs464637; hg19: chr5-2340989;