15-32716669-T-C

Variant names:

• chr15-32716669-T-C
• rs3812934

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 0.423 in 151,880 control chromosomes in the GnomAD database, including 13,953 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 0.42 (13953 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.481 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: 0.424 AC: 64286 AN: 151762 Hom.: 13952 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.423 AC: 64311 AN: 151880 Hom.: 13953 Cov.: 31 AF XY: 0.422 AC XY: 31313 AN XY: 74240

African (AFR) AF: 0.356 AC: 14715 AN: 41384

American (AMR) AF: 0.491 AC: 7492 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1846 AN: 3466

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5160

South Asian (SAS) AF: 0.421 AC: 2025 AN: 4814

European-Finnish (FIN) AF: 0.412 AC: 4332 AN: 10518

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30838 AN: 67962

Other (OTH) AF: 0.422 AC: 887 AN: 2104

Alfa AF: 0.446 Hom.: 57961

Bravo AF: 0.427

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.17
DANN	Benign	0.32
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3812934; hg19: chr15-33008870;