15-45426989-G-C

Position:

• chr15-45426989-G-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 0.461 in 152,046 control chromosomes in the GnomAD database, including 17,372 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 (17372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70063 AN: 151930 Hom.: 17358 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.461 AC: 70107 AN: 152046 Hom.: 17372 Cov.: 32 AF XY: 0.473 AC XY: 35153 AN XY: 74318

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.503

Alfa AF: 0.270 Hom.: 609

Bravo AF: 0.472

Asia WGS AF: 0.689 AC: 2391 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17536527; hg19: chr15-45719187;