9-117687188-A-G

Variant names:

• chr9-117687188-A-G
• rs1360094

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 0.526 in 151,722 control chromosomes in the GnomAD database, including 23,681 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 0.53 (23681 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79854 AN: 151602 Hom.: 23688 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.526 AC: 79857 AN: 151722 Hom.: 23681 Cov.: 31 AF XY: 0.525 AC XY: 38904 AN XY: 74128

African (AFR) AF: 0.231 AC: 9577 AN: 41428

American (AMR) AF: 0.586 AC: 8901 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2145 AN: 3466

East Asian (EAS) AF: 0.618 AC: 3159 AN: 5108

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4816

European-Finnish (FIN) AF: 0.553 AC: 5844 AN: 10560

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45193 AN: 67840

Other (OTH) AF: 0.570 AC: 1199 AN: 2102

Alfa AF: 0.625 Hom.: 95802

Bravo AF: 0.519

Asia WGS AF: 0.592 AC: 2060 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.42
DANN	Benign	0.75
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1360094; hg19: chr9-120449466;