15-45360505-C-T

Variant names:

• chr15-45360505-C-T
• rs1153858

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 0.461 in 151,892 control chromosomes in the GnomAD database, including 20,431 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 0.46 (20431 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.461 AC: 69977 AN: 151774 Hom.: 20369 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.461 AC: 70097 AN: 151892 Hom.: 20431 Cov.: 31 AF XY: 0.466 AC XY: 34560 AN XY: 74220

African (AFR) AF: 0.784 AC: 32508 AN: 41484

American (AMR) AF: 0.516 AC: 7877 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3466

East Asian (EAS) AF: 0.836 AC: 4327 AN: 5178

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3265 AN: 10478

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17757 AN: 67898

Other (OTH) AF: 0.446 AC: 938 AN: 2104

Alfa AF: 0.370 Hom.: 23228

Bravo AF: 0.496

Asia WGS AF: 0.628 AC: 2181 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	5.1
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1153858; hg19: chr15-45652703;