9-114760770-T-C

Variant names:

• chr9-114760770-T-C
• rs10733612

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 0.762 in 152,140 control chromosomes in the GnomAD database, including 44,257 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 0.76 (44257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.762 AC: 115791 AN: 152024 Hom.: 44225 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.762 AC: 115876 AN: 152140 Hom.: 44257 Cov.: 32 AF XY: 0.766 AC XY: 56943 AN XY: 74368

African (AFR) AF: 0.732 AC: 30377 AN: 41478

American (AMR) AF: 0.769 AC: 11752 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2822 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4322 AN: 5168

South Asian (SAS) AF: 0.831 AC: 4007 AN: 4824

European-Finnish (FIN) AF: 0.821 AC: 8695 AN: 10596

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.756 AC: 51431 AN: 68010

Other (OTH) AF: 0.768 AC: 1624 AN: 2114

Alfa AF: 0.747 Hom.: 5474

Bravo AF: 0.757

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.78
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10733612; hg19: chr9-117523050; COSMIC: COSV60395585;