rs10983754

Variant names:

• chr9-117696329-C-T
• rs10983754

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 0.0893 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
• Publications: 8 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.132 AC: 5473 AN: 41498

American (AMR) AF: 0.0604 AC: 924 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5162

South Asian (SAS) AF: 0.119 AC: 572 AN: 4820

European-Finnish (FIN) AF: 0.101 AC: 1064 AN: 10586

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0755 AC: 5135 AN: 67984

Other (OTH) AF: 0.0818 AC: 173 AN: 2114

Alfa AF: 0.0803 Hom.: 111

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10983754; hg19: chr9-120458607;