15-54667075-C-G

Position:

• chr15-54667075-C-G

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 0.737 in 152,160 control chromosomes in the GnomAD database, including 41,434 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 0.74 (41434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 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: 0.737 AC: 112027 AN: 152042 Hom.: 41392 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.737 AC: 112122 AN: 152160 Hom.: 41434 Cov.: 32 AF XY: 0.738 AC XY: 54899 AN XY: 74408

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.727

Alfa AF: 0.744 Hom.: 5223

Bravo AF: 0.724

Asia WGS AF: 0.758 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2414351; hg19: chr15-54959273;