rs3115576

Variant names:

• chr6-32249073-T-A
• rs3115576

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.343 AC: 14217 AN: 41462

American (AMR) AF: 0.513 AC: 7845 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2222 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2455 AN: 5172

South Asian (SAS) AF: 0.574 AC: 2769 AN: 4824

European-Finnish (FIN) AF: 0.275 AC: 2910 AN: 10596

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29190 AN: 67964

Other (OTH) AF: 0.447 AC: 945 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3115576; hg19: chr6-32216850;