rs9261519

Positions:

• chr6-30149324-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;