9-117688520-A-G

Variant names:

• chr9-117688520-A-G
• rs4837496

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 0.626 in 151,522 control chromosomes in the GnomAD database, including 31,410 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 0.63 (31410 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 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: 0.626 AC: 94830 AN: 151404 Hom.: 31417 Cov.: 30

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.626 AC: 94852 AN: 151522 Hom.: 31410 Cov.: 30 AF XY: 0.626 AC XY: 46349 AN XY: 74026

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.661

Alfa AF: 0.728 Hom.: 79891

Bravo AF: 0.615

Asia WGS AF: 0.676 AC: 2350 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837496; hg19: chr9-120450798;