chr9-113765903-T-C

Variant names:

• chr9-113765903-T-C
• rs7868736

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 0.732 in 151,996 control chromosomes in the GnomAD database, including 40,997 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 0.73 (40997 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 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: 0.731 AC: 111088 AN: 151876 Hom.: 40943 Cov.: 30

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.732 AC: 111196 AN: 151996 Hom.: 40997 Cov.: 30 AF XY: 0.734 AC XY: 54520 AN XY: 74298

African (AFR) AF: 0.714 AC: 29587 AN: 41438

American (AMR) AF: 0.791 AC: 12078 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5013 AN: 5172

South Asian (SAS) AF: 0.807 AC: 3880 AN: 4806

European-Finnish (FIN) AF: 0.724 AC: 7645 AN: 10558

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48273 AN: 67962

Other (OTH) AF: 0.741 AC: 1566 AN: 2114

Alfa AF: 0.724 Hom.: 175158

Bravo AF: 0.738

Asia WGS AF: 0.869 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.9
DANN	Benign	0.78
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7868736; hg19: chr9-116528183; COSMIC: COSV60395312;