rs4498613

Variant names:

• chr9-93743357-A-C
• rs4498613

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 0.136 in 152,214 control chromosomes in the GnomAD database, including 1,762 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 0.14 (1762 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.136 AC: 20656 AN: 152096 Hom.: 1764 Cov.: 31

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.136 AC: 20661 AN: 152214 Hom.: 1762 Cov.: 31 AF XY: 0.138 AC XY: 10254 AN XY: 74416

African (AFR) AF: 0.0412 AC: 1711 AN: 41534

American (AMR) AF: 0.138 AC: 2103 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3472

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5182

South Asian (SAS) AF: 0.166 AC: 802 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2488 AN: 10594

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

European-Non Finnish (NFE) AF: 0.180 AC: 12246 AN: 68000

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.161 Hom.: 1844

Bravo AF: 0.122

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4498613; hg19: chr9-96505639; COSMIC: COSV107153953;