rs3115576

Variant names:

• chr6-32249073-T-A
• rs3115576

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 0.415 in 152,100 control chromosomes in the GnomAD database, including 13,636 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 0.41 (13636 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.415 AC: 63074 AN: 151982 Hom.: 13626 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.415 AC: 63107 AN: 152100 Hom.: 13636 Cov.: 33 AF XY: 0.414 AC XY: 30754 AN XY: 74364

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.447

Alfa AF: 0.413 Hom.: 1724

Bravo AF: 0.428

Asia WGS AF: 0.469 AC: 1635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3115576; hg19: chr6-32216850;