rs9261519

Variant names:

• chr6-30149324-T-C
• rs9261519

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 0.22 in 152,150 control chromosomes in the GnomAD database, including 4,028 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 (4028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

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 (AMR) allele frequency at 95% confidence interval = 0.25 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: 0.220 AC: 33466 AN: 152030 Hom.: 4026 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.220 AC: 33485 AN: 152150 Hom.: 4028 Cov.: 32 AF XY: 0.222 AC XY: 16480 AN XY: 74380

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.187

Alfa AF: 0.239 Hom.: 3215

Bravo AF: 0.213

Asia WGS AF: 0.153 AC: 533 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	4.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261519; hg19: chr6-30117101;