15-53236233-T-C

Variant names:

• chr15-53236233-T-C
• rs4109297

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.627 AC: 25842 AN: 41232

American (AMR) AF: 0.783 AC: 11784 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2515 AN: 3420

East Asian (EAS) AF: 0.571 AC: 2854 AN: 4994

South Asian (SAS) AF: 0.724 AC: 3414 AN: 4718

European-Finnish (FIN) AF: 0.913 AC: 9647 AN: 10564

Middle Eastern (MID) AF: 0.734 AC: 213 AN: 290

European-Non Finnish (NFE) AF: 0.844 AC: 56625 AN: 67098

Other (OTH) AF: 0.761 AC: 1588 AN: 2086

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4109297; hg19: chr15-53528430;