chr9-29545877-C-T

Variant names:

• chr9-29545877-C-T
• rs13290799

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 0.14 in 152,070 control chromosomes in the GnomAD database, including 1,669 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 0.14 (1669 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.140 AC: 21282 AN: 151952 Hom.: 1668 Cov.: 31

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.0870

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.140 AC: 21304 AN: 152070 Hom.: 1669 Cov.: 31 AF XY: 0.139 AC XY: 10331 AN XY: 74296

Gnomad4 AFR AF: 0.0838

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0722

Gnomad4 SAS AF: 0.0974

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.161

Alfa AF: 0.163 Hom.: 4245

Bravo AF: 0.135

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290799; hg19: chr9-29545875;