rs10732345

Variant names:

• chr9-24788181-G-A
• rs10732345

Your query was ambiguous. Multiple possible variants found:

• chr9-24788181-G-A
• chr9-24788181-G-C

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 0.592 in 151,080 control chromosomes in the GnomAD database, including 27,287 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 0.59 (27287 hom., cov: 31)
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.592 AC: 89325 AN: 150960 Hom.: 27243 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.625

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.592 AC: 89424 AN: 151080 Hom.: 27287 Cov.: 31 AF XY: 0.591 AC XY: 43577 AN XY: 73768

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.598

Alfa AF: 0.542 Hom.: 36699

Bravo AF: 0.607

Asia WGS AF: 0.720 AC: 2502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10732345; hg19: chr9-24788179; COSMIC: COSV60343381;