rs9261926

chr6-30424629-C-Achr6-30424629-C-Gchr6-30424629-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 0.184 in 134,300 control chromosomes in the GnomAD database, including 2,197 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 0.18 (2197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.184 AC: 24701 AN: 134180 Hom.: 2197 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.184 AC: 24716 AN: 134300 Hom.: 2197 Cov.: 31 AF XY: 0.181 AC XY: 11725 AN XY: 64714

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0400

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.172

Alfa AF: 0.142 Hom.: 1161

Bravo AF: 0.171

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.2
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261926; hg19: chr6-30392406;