rs10733612

Variant names:

• chr9-114760770-T-C
• rs10733612

Your query was ambiguous. Multiple possible variants found:

• chr9-114760770-T-C
• chr9-114760770-T-G

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 0.762 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.768

Alfa AF: 0.749 Hom.: 5282

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

Splicing

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

Publications

LitVar

Other links and lift over

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