rs10519239

chr15-49794283-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000558657.1(ENSG00000259388):n.38C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0254 in 1,151,916 control chromosomes in the GnomAD database, including 536 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 0.036 (110 hom., cov: 32)
  • Exomes 𝑓: 0.024 (426 hom.)
• Consequence: ENST00000558657.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0358 (5455/152270) while in subpopulation AMR AF= 0.0422 (646/15296). AF 95% confidence interval is 0.0395. There are 110 homozygotes in gnomad4. There are 2558 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000558657.1	n.38C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5455 AN: 152152 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0392

GnomAD4 exome AF: 0.0238 AC: 23748 AN: 999646 Hom.: 426 Cov.: 15 AF XY: 0.0240 AC XY: 12395 AN XY: 517028

Gnomad4 AFR exome AF: 0.0284

Gnomad4 AMR exome AF: 0.0285

Gnomad4 ASJ exome AF: 0.0579

Gnomad4 EAS exome AF: 0.0000797

Gnomad4 SAS exome AF: 0.0135

Gnomad4 FIN exome AF: 0.0183

Gnomad4 NFE exome AF: 0.0247

Gnomad4 OTH exome AF: 0.0282

GnomAD4 genome AF: 0.0358 AC: 5455 AN: 152270 Hom.: 110 Cov.: 32 AF XY: 0.0343 AC XY: 2558 AN XY: 74470

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.0422

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.0406

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0386 Hom.: 124

Bravo AF: 0.0355

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	3.7
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519239; hg19: chr15-50086480;