rs9260759

chr6-29967595-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 0.134 in 151,782 control chromosomes in the GnomAD database, including 1,615 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 0.13 (1615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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: 0.133 AC: 20232 AN: 151666 Hom.: 1612 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.134 AC: 20263 AN: 151782 Hom.: 1615 Cov.: 32 AF XY: 0.133 AC XY: 9859 AN XY: 74206

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0711

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.144

Alfa AF: 0.118 Hom.: 898

Bravo AF: 0.143

Asia WGS AF: 0.0930 AC: 323 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.5
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9260759; hg19: chr6-29935372;