rs4641026

Variant names:

• chr8-127516288-G-A
• rs4641026

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 0.811 in 151,982 control chromosomes in the GnomAD database, including 50,661 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 0.81 (50661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 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: 0.812 AC: 123247 AN: 151864 Hom.: 50639 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.811 AC: 123313 AN: 151982 Hom.: 50661 Cov.: 32 AF XY: 0.810 AC XY: 60176 AN XY: 74282

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.841

Alfa AF: 0.855 Hom.: 13900

Bravo AF: 0.807

Asia WGS AF: 0.743 AC: 2567 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4641026; hg19: chr8-128528533;