chr9-117671123-T-C

Variant names:

• chr9-117671123-T-C
• rs10818066

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 0.268 in 151,976 control chromosomes in the GnomAD database, including 5,727 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 0.27 (5727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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: 0.268 AC: 40693 AN: 151858 Hom.: 5707 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.268 AC: 40766 AN: 151976 Hom.: 5727 Cov.: 32 AF XY: 0.266 AC XY: 19798 AN XY: 74290

African (AFR) AF: 0.334 AC: 13831 AN: 41420

American (AMR) AF: 0.325 AC: 4953 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1777 AN: 5152

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4812

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10576

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15713 AN: 67982

Other (OTH) AF: 0.273 AC: 574 AN: 2106

Alfa AF: 0.245 Hom.: 19032

Bravo AF: 0.281

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10818066; hg19: chr9-120433401;