8-59143670-A-G

Variant names:

• chr8-59143670-A-G
• rs4738757

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 0.48 in 152,014 control chromosomes in the GnomAD database, including 18,202 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 0.48 (18202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 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: 0.480 AC: 72870 AN: 151896 Hom.: 18183 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.480 AC: 72941 AN: 152014 Hom.: 18202 Cov.: 31 AF XY: 0.470 AC XY: 34953 AN XY: 74320

African (AFR) AF: 0.549 AC: 22743 AN: 41436

American (AMR) AF: 0.577 AC: 8823 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3468

East Asian (EAS) AF: 0.546 AC: 2816 AN: 5158

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4822

European-Finnish (FIN) AF: 0.289 AC: 3062 AN: 10578

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30618 AN: 67960

Other (OTH) AF: 0.514 AC: 1086 AN: 2112

Alfa AF: 0.474 Hom.: 70946

Bravo AF: 0.513

Asia WGS AF: 0.430 AC: 1497 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	0.85
DANN	Benign	0.69
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4738757; hg19: chr8-60056229;