rs9295794

chr6-29137158-G-Achr6-29137158-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 0.0808 in 151,920 control chromosomes in the GnomAD database, including 575 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 0.081 (575 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0929 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: 0.0809 AC: 12276 AN: 151798 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0288

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0808 AC: 12280 AN: 151920 Hom.: 575 Cov.: 32 AF XY: 0.0815 AC XY: 6049 AN XY: 74246

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0926

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0885

Gnomad4 OTH AF: 0.0860

Alfa AF: 0.0770 Hom.: 333

Bravo AF: 0.0826

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.2
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295794; hg19: chr6-29104935;