rs9294536

Variant names:

• chr6-92810539-C-A
• rs9294536

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 0.389 in 151,982 control chromosomes in the GnomAD database, including 12,319 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 0.39 (12319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.388 AC: 58988 AN: 151866 Hom.: 12294 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.389 AC: 59058 AN: 151982 Hom.: 12319 Cov.: 32 AF XY: 0.384 AC XY: 28508 AN XY: 74264

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.396

Alfa AF: 0.353 Hom.: 14407

Bravo AF: 0.392

Asia WGS AF: 0.279 AC: 965 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9294536; hg19: chr6-93520257;