rs749492

Variant names:

• chr8-117562391-A-G
• rs749492

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 0.125 in 152,174 control chromosomes in the GnomAD database, including 1,443 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 0.13 (1443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.125 AC: 19070 AN: 152056 Hom.: 1445 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.125 AC: 19063 AN: 152174 Hom.: 1443 Cov.: 32 AF XY: 0.125 AC XY: 9284 AN XY: 74390

African (AFR) AF: 0.0477 AC: 1981 AN: 41550

American (AMR) AF: 0.142 AC: 2165 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.0625 AC: 324 AN: 5180

South Asian (SAS) AF: 0.0668 AC: 322 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1853 AN: 10588

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11499 AN: 67966

Other (OTH) AF: 0.139 AC: 293 AN: 2106

Alfa AF: 0.157 Hom.: 2444

Bravo AF: 0.124

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs749492; hg19: chr8-118574630;