rs10739427

Positions:

• chr9-114734055-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 0.768 in 152,096 control chromosomes in the GnomAD database, including 44,983 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 0.77 (44983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116742 AN: 151978 Hom.: 44946 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.768 AC: 116835 AN: 152096 Hom.: 44983 Cov.: 32 AF XY: 0.772 AC XY: 57450 AN XY: 74372

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.772

Alfa AF: 0.753 Hom.: 5344

Bravo AF: 0.764

Asia WGS AF: 0.811 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10739427; hg19: chr9-117496335; COSMIC: COSV60395525;