rs10988653

Variant names:

• chr9-130244195-T-C
• rs10988653

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 0.321 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.217 AC: 9014 AN: 41454

American (AMR) AF: 0.289 AC: 4421 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3464

East Asian (EAS) AF: 0.0614 AC: 317 AN: 5162

South Asian (SAS) AF: 0.421 AC: 2026 AN: 4816

European-Finnish (FIN) AF: 0.354 AC: 3741 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26819 AN: 67888

Other (OTH) AF: 0.335 AC: 709 AN: 2114

Alfa AF: 0.369 Hom.: 42538

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
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10988653; hg19: chr9-133006474;