rs3118520

Variant names:

• chr9-134549749-A-G
• rs3118520

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 152,224 control chromosomes in the GnomAD database, including 19,988 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 (19988 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 72947 AN: 152106 Hom.: 19943 Cov.: 35

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.480 AC: 73053 AN: 152224 Hom.: 19988 Cov.: 35 AF XY: 0.474 AC XY: 35277 AN XY: 74426

African (AFR) AF: 0.758 AC: 31520 AN: 41556

American (AMR) AF: 0.393 AC: 6010 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1563 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1090 AN: 5180

South Asian (SAS) AF: 0.521 AC: 2513 AN: 4820

European-Finnish (FIN) AF: 0.280 AC: 2962 AN: 10596

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 26003 AN: 68002

Other (OTH) AF: 0.469 AC: 992 AN: 2114

Alfa AF: 0.415 Hom.: 48175

Bravo AF: 0.496

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.50
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs3118520; hg19: chr9-137441595;