rs3118523

Variant names:

• chr9-134443675-G-A
• rs3118523

Your query was ambiguous. Multiple possible variants found:

• chr9-134443675-G-A
• chr9-134443675-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.748 in 152,016 control chromosomes in the GnomAD database, including 43,053 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 0.75 (43053 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.749 AC: 113727 AN: 151898 Hom.: 43054 Cov.: 34

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.748 AC: 113762 AN: 152016 Hom.: 43053 Cov.: 34 AF XY: 0.748 AC XY: 55540 AN XY: 74290

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.734

Alfa AF: 0.780 Hom.: 19042

Bravo AF: 0.739

Asia WGS AF: 0.653 AC: 2267 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.0
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118523; hg19: chr9-137335521; COSMIC: COSV62683936;