15-40593559-T-C

Position:

• chr15-40593559-T-C

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 0.123 in 152,100 control chromosomes in the GnomAD database, including 1,598 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 0.12 (1598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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: 0.122 AC: 18598 AN: 151982 Hom.: 1590 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.123 AC: 18638 AN: 152100 Hom.: 1598 Cov.: 32 AF XY: 0.121 AC XY: 8981 AN XY: 74354

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.0692

Gnomad4 OTH AF: 0.105

Alfa AF: 0.107 Hom.: 195

Bravo AF: 0.128

Asia WGS AF: 0.110 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8034726; hg19: chr15-40885757;