chr9-113765903-T-C

Variant names:

• chr9-113765903-T-C
• rs7868736

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 0.732 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.741

Alfa AF: 0.723 Hom.: 82580

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

Splicing

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

Publications

LitVar

Other links and lift over

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