15-59737814-C-T

Variant names:

• chr15-59737814-C-T
• rs4620904

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 0.141 in 152,050 control chromosomes in the GnomAD database, including 1,901 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 0.14 (1901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 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: 0.142 AC: 21502 AN: 151934 Hom.: 1900 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.141 AC: 21497 AN: 152050 Hom.: 1901 Cov.: 32 AF XY: 0.144 AC XY: 10724 AN XY: 74302

Gnomad4 AFR AF: 0.0337

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.170

Alfa AF: 0.174 Hom.: 1188

Bravo AF: 0.132

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4620904; hg19: chr15-60030013;