chr15-32745434-C-T

Variant names:

• chr15-32745434-C-T
• rs11631292

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0609 in 152,264 control chromosomes in the GnomAD database, including 421 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 0.061 (421 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0803 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: 0.0610 AC: 9283 AN: 152146 Hom.: 421 Cov.: 31

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0609 AC: 9280 AN: 152264 Hom.: 421 Cov.: 31 AF XY: 0.0626 AC XY: 4664 AN XY: 74446

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0600

Gnomad4 ASJ AF: 0.0887

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0738 Hom.: 104

Bravo AF: 0.0545

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	8.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11631292; hg19: chr15-33037635;