rs10971969

chr9-34164377-A-Gchr9-34164377-A-T

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 0.126 in 146,912 control chromosomes in the GnomAD database, including 1,487 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 0.13 (1487 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 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: 0.126 AC: 18463 AN: 146888 Hom.: 1487 Cov.: 30

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.126 AC: 18452 AN: 146912 Hom.: 1487 Cov.: 30 AF XY: 0.122 AC XY: 8710 AN XY: 71252

Gnomad4 AFR AF: 0.0343

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.130

Alfa AF: 0.139 Hom.: 347

Bravo AF: 0.116

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	7.1
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10971969; hg19: chr9-34164375; COSMIC: COSV53375528;