9-117688520-A-G

Variant names:

• chr9-117688520-A-G
• rs4837496

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 0.626 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.392 AC: 16185 AN: 41336

American (AMR) AF: 0.654 AC: 9941 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2364 AN: 3462

East Asian (EAS) AF: 0.620 AC: 3163 AN: 5098

South Asian (SAS) AF: 0.732 AC: 3527 AN: 4816

European-Finnish (FIN) AF: 0.656 AC: 6880 AN: 10486

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50462 AN: 67806

Other (OTH) AF: 0.661 AC: 1393 AN: 2108

Alfa AF: 0.715 Hom.: 161219

Bravo AF: 0.615

Asia WGS AF: 0.676 AC: 2350 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4837496; hg19: chr9-120450798;