rs13290799

Positions:

• chr9-29545877-C-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 0.14 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;