chr15-32707605-C-T

Position:

• chr15-32707605-C-T

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 0.67 in 151,924 control chromosomes in the GnomAD database, including 36,180 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 0.67 (36180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101647 AN: 151806 Hom.: 36157 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.670 AC: 101716 AN: 151924 Hom.: 36180 Cov.: 31 AF XY: 0.665 AC XY: 49376 AN XY: 74250

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.708

Alfa AF: 0.761 Hom.: 10611

Bravo AF: 0.664

Asia WGS AF: 0.429 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554865; hg19: chr15-32999806;