rs4524788

Variant names:

• chr8-83718986-G-A
• rs4524788

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 0.588 in 151,710 control chromosomes in the GnomAD database, including 26,578 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 0.59 (26578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 3 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 = 0.826 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: 0.588 AC: 89162 AN: 151594 Hom.: 26556 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.588 AC: 89234 AN: 151710 Hom.: 26578 Cov.: 31 AF XY: 0.591 AC XY: 43822 AN XY: 74146

African (AFR) AF: 0.530 AC: 21935 AN: 41374

American (AMR) AF: 0.630 AC: 9595 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1933 AN: 3468

East Asian (EAS) AF: 0.847 AC: 4382 AN: 5172

South Asian (SAS) AF: 0.545 AC: 2622 AN: 4808

European-Finnish (FIN) AF: 0.633 AC: 6640 AN: 10494

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40362 AN: 67860

Other (OTH) AF: 0.570 AC: 1195 AN: 2098

Alfa AF: 0.590 Hom.: 13130

Bravo AF: 0.589

Asia WGS AF: 0.699 AC: 2423 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs4524788; hg19: chr8-84631221;