15-60324736-T-G

Position:

• chr15-60324736-T-G

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 0.379 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.60324736T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.390

Alfa AF: 0.385 Hom.: 5583

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033028; hg19: chr15-60616935;