rs4641026

chr8-127516288-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 0.811 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;