9-29469229-C-T

Variant names:

• chr9-29469229-C-T
• rs10969189

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 0.028 in 143,390 control chromosomes in the GnomAD database, including 97 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 0.028 (97 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0769 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: 0.0279 AC: 3996 AN: 143356 Hom.: 94 Cov.: 30

Gnomad AFR AF: 0.00940

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.0163

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0408

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0232

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

GnomAD4 genome AF: 0.0280 AC: 4011 AN: 143390 Hom.: 97 Cov.: 30 AF XY: 0.0275 AC XY: 1907 AN XY: 69310

Gnomad4 AFR AF: 0.00972

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0163

Gnomad4 EAS AF: 0.0836

Gnomad4 SAS AF: 0.0281

Gnomad4 FIN AF: 0.0252

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0230

Alfa AF: 0.0120 Hom.: 1

Bravo AF: 0.0285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.61
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10969189; hg19: chr9-29469227; COSMIC: COSV69457338;