rs10969148

chr9-29417719-T-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 0.0417 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;