rs10983754

chr9-117696329-C-T

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 0.0893 in 152,130 control chromosomes in the GnomAD database, including 697 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 0.089 (697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13577 AN: 152012 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0893 AC: 13586 AN: 152130 Hom.: 697 Cov.: 32 AF XY: 0.0905 AC XY: 6734 AN XY: 74372

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.000969

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0755

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0792 Hom.: 106

Bravo AF: 0.0845

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.42
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10983754; hg19: chr9-120458607;