rs10969148

Variant names:

• chr9-29417719-T-A
• rs10969148

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 0.0417 in 150,626 control chromosomes in the GnomAD database, including 184 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 0.042 (184 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0818 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: 0.0416 AC: 6257 AN: 150510 Hom.: 180 Cov.: 30

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0250

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0417 AC: 6284 AN: 150626 Hom.: 184 Cov.: 30 AF XY: 0.0411 AC XY: 3023 AN XY: 73538

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.0250

Gnomad4 EAS AF: 0.0885

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0392 Hom.: 20

Asia WGS AF: 0.0530 AC: 186 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10969148; hg19: chr9-29417717; COSMIC: COSV69456978;