15-50871860-C-T

Position:

• chr15-50871860-C-T

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 0.294 in 151,988 control chromosomes in the GnomAD database, including 6,773 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 0.29 (6773 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50871860C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000273674	ENST00000613161.4	n.425+2712G>A		intron_variant		2
ENSG00000273674	ENST00000617693.4	n.243+2712G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44613 AN: 151870 Hom.: 6763 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.294 AC: 44658 AN: 151988 Hom.: 6773 Cov.: 32 AF XY: 0.292 AC XY: 21688 AN XY: 74292

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.272

Alfa AF: 0.305 Hom.: 860

Bravo AF: 0.297

Asia WGS AF: 0.294 AC: 1021 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	0.42
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4142324; hg19: chr15-51164057;