chr15-32716669-T-C

Variant names:

• chr15-32716669-T-C
• rs3812934

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 0.423 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.424 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

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.422

Alfa AF: 0.445 Hom.: 25358

Bravo AF: 0.427

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3812934; hg19: chr15-33008870;