15-53236233-T-C

Position:

• chr15-53236233-T-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 0.767 in 150,344 control chromosomes in the GnomAD database, including 44,521 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 0.77 (44521 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 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: 0.767 AC: 115202 AN: 150232 Hom.: 44507 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.767 AC: 115258 AN: 150344 Hom.: 44521 Cov.: 33 AF XY: 0.768 AC XY: 56418 AN XY: 73496

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.761

Alfa AF: 0.815 Hom.: 9254

Bravo AF: 0.750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4109297; hg19: chr15-53528430;