rs9261799

Variant names:

• chr6-30408710-C-T
• rs9261799

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 0.161 in 152,012 control chromosomes in the GnomAD database, including 2,123 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 0.16 (2123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24420 AN: 151894 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.161 AC: 24442 AN: 152012 Hom.: 2123 Cov.: 32 AF XY: 0.156 AC XY: 11623 AN XY: 74316

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.157

Alfa AF: 0.161 Hom.: 632

Bravo AF: 0.168

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261799; hg19: chr6-30376487;