rs9260734

chr6-29964889-G-A

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 0.216 in 151,476 control chromosomes in the GnomAD database, including 3,966 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 0.22 (3966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804

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 (AFR) allele frequency at 95% confidence interval = 0.313 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: 0.216 AC: 32623 AN: 151362 Hom.: 3954 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.216 AC: 32656 AN: 151476 Hom.: 3966 Cov.: 32 AF XY: 0.217 AC XY: 16052 AN XY: 74048

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.219

Alfa AF: 0.170 Hom.: 3171

Bravo AF: 0.227

Asia WGS AF: 0.240 AC: 829 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	0.51
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9260734; hg19: chr6-29932666;