chr15-74745879-G-A

Position:

• chr15-74745879-G-A

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 0.127 in 152,038 control chromosomes in the GnomAD database, including 2,533 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Pathogenic (no stars).

• Frequency: Genomes: 𝑓 0.13 (2533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.127 AC: 19233 AN: 151920 Hom.: 2514 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.127 AC: 19303 AN: 152038 Hom.: 2533 Cov.: 32 AF XY: 0.131 AC XY: 9698 AN XY: 74302

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.0490

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0727 Hom.: 163

Bravo AF: 0.153

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069514; hg19: chr15-75038220;