15-45975700-A-T

Position:

• chr15-45975700-A-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 0.337 in 152,042 control chromosomes in the GnomAD database, including 11,129 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 0.34 (11129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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: 0.337 AC: 51227 AN: 151922 Hom.: 11096 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.337 AC: 51302 AN: 152042 Hom.: 11129 Cov.: 32 AF XY: 0.332 AC XY: 24681 AN XY: 74334

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.278

Alfa AF: 0.316 Hom.: 1146

Bravo AF: 0.341

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs939394; hg19: chr15-46267898;