rs10739427

Variant names:

• chr9-114734055-T-G
• rs10739427

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 0.768 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.756 AC: 31358 AN: 41470

American (AMR) AF: 0.773 AC: 11817 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4328 AN: 5180

South Asian (SAS) AF: 0.827 AC: 3991 AN: 4824

European-Finnish (FIN) AF: 0.819 AC: 8664 AN: 10576

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51281 AN: 67974

Other (OTH) AF: 0.772 AC: 1626 AN: 2106

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

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