rs10983755

chr9-117702392-G-A

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 0.0353 in 152,242 control chromosomes in the GnomAD database, including 237 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 0.035 (237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.0353 AC: 5365 AN: 152124 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0353 AC: 5367 AN: 152242 Hom.: 237 Cov.: 32 AF XY: 0.0386 AC XY: 2870 AN XY: 74434

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0274 Hom.: 22

Bravo AF: 0.0332

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
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: rs10983755; hg19: chr9-120464670;