15-45360505-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 0.461 in 151,892 control chromosomes in the GnomAD database, including 20,431 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 0.46 (20431 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.461 AC: 69977 AN: 151774 Hom.: 20369 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.461 AC: 70097 AN: 151892 Hom.: 20431 Cov.: 31 AF XY: 0.466 AC XY: 34560 AN XY: 74220

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.446

Alfa AF: 0.375 Hom.: 3038

Bravo AF: 0.496

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1153858; hg19: chr15-45652703;