15-60324736-T-G

Variant names:

• chr15-60324736-T-G
• rs1033028

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 0.379 in 152,080 control chromosomes in the GnomAD database, including 11,416 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 0.38 (11416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.516 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: 0.379 AC: 57570 AN: 151962 Hom.: 11407 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.379 AC: 57599 AN: 152080 Hom.: 11416 Cov.: 32 AF XY: 0.379 AC XY: 28200 AN XY: 74342

African (AFR) AF: 0.277 AC: 11476 AN: 41454

American (AMR) AF: 0.525 AC: 8032 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2222 AN: 5176

South Asian (SAS) AF: 0.405 AC: 1955 AN: 4826

European-Finnish (FIN) AF: 0.374 AC: 3959 AN: 10576

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27180 AN: 67986

Other (OTH) AF: 0.390 AC: 821 AN: 2106

Alfa AF: 0.386 Hom.: 6227

Bravo AF: 0.390

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.51
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs1033028; hg19: chr15-60616935;