rs4601326

Variant names:

• chr8-130479982-A-G
• rs4601326

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 0.762 in 152,020 control chromosomes in the GnomAD database, including 44,313 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 0.76 (44313 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.762 AC: 115754 AN: 151902 Hom.: 44261 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.762 AC: 115872 AN: 152020 Hom.: 44313 Cov.: 30 AF XY: 0.758 AC XY: 56344 AN XY: 74290

African (AFR) AF: 0.830 AC: 34400 AN: 41448

American (AMR) AF: 0.713 AC: 10890 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3359 AN: 5168

South Asian (SAS) AF: 0.717 AC: 3455 AN: 4822

European-Finnish (FIN) AF: 0.747 AC: 7883 AN: 10552

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50818 AN: 67966

Other (OTH) AF: 0.738 AC: 1555 AN: 2108

Alfa AF: 0.750 Hom.: 73856

Bravo AF: 0.765

Asia WGS AF: 0.708 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4601326; hg19: chr8-131492228;