rs10969194

chr9-29472998-G-Achr9-29472998-G-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 0.027 in 152,218 control chromosomes in the GnomAD database, including 96 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 0.027 (96 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0762 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: 0.0269 AC: 4094 AN: 152100 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00930

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0270 AC: 4108 AN: 152218 Hom.: 96 Cov.: 32 AF XY: 0.0265 AC XY: 1971 AN XY: 74432

Gnomad4 AFR AF: 0.00958

Gnomad4 AMR AF: 0.0235

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.0827

Gnomad4 SAS AF: 0.0264

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0123 Hom.: 1

Bravo AF: 0.0287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	4.5
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10969194; hg19: chr9-29472996; COSMIC: COSV69457366;