rs4531042

Variant names:

• chr8-59176129-G-A
• rs4531042

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 0.393 in 152,028 control chromosomes in the GnomAD database, including 12,342 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 0.39 (12342 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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: 0.393 AC: 59723 AN: 151910 Hom.: 12331 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.393 AC: 59774 AN: 152028 Hom.: 12342 Cov.: 32 AF XY: 0.387 AC XY: 28794 AN XY: 74346

African (AFR) AF: 0.395 AC: 16388 AN: 41446

American (AMR) AF: 0.525 AC: 8027 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2822 AN: 5178

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4818

European-Finnish (FIN) AF: 0.236 AC: 2500 AN: 10580

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25787 AN: 67944

Other (OTH) AF: 0.440 AC: 928 AN: 2110

Alfa AF: 0.383 Hom.: 6774

Bravo AF: 0.422

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.28
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs4531042; hg19: chr8-60088688;