rs10988653

chr9-130244195-T-C

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 0.321 in 151,958 control chromosomes in the GnomAD database, including 8,570 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 0.32 (8570 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 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: 0.321 AC: 48792 AN: 151840 Hom.: 8569 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.321 AC: 48817 AN: 151958 Hom.: 8570 Cov.: 31 AF XY: 0.319 AC XY: 23719 AN XY: 74274

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.0614

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.335

Alfa AF: 0.382 Hom.: 20350

Bravo AF: 0.308

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	6.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10988653; hg19: chr9-133006474;