rs467259

Variant names:

• chr5-6026264-G-A
• rs467259

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 0.178 in 152,046 control chromosomes in the GnomAD database, including 2,935 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 0.18 (2935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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: 0.178 AC: 27081 AN: 151928 Hom.: 2928 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0251

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.178 AC: 27121 AN: 152046 Hom.: 2935 Cov.: 32 AF XY: 0.176 AC XY: 13057 AN XY: 74294

African (AFR) AF: 0.305 AC: 12645 AN: 41440

American (AMR) AF: 0.110 AC: 1686 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5176

South Asian (SAS) AF: 0.136 AC: 653 AN: 4812

European-Finnish (FIN) AF: 0.146 AC: 1542 AN: 10572

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9409 AN: 67980

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.175 Hom.: 337

Bravo AF: 0.177

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.66
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs467259; hg19: chr5-6026377;