15-20352408-C-T

Variant names:

• chr15-20352408-C-T
• rs1039353
• ENST00000557528.1:n.48C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557528.1(ENSG00000258654):​n.48C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.42 (2117 hom., cov: 98)
  • Exomes 𝑓: 0.40 (93 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000258654 ENST00000557528.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

ENSG00000258654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.404 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
ENSG00000258654	ENST00000557528.1	n.48C>T		non_coding_transcript_exon_variant	Exon 1 of 2	5
ENSG00000258654	ENST00000554815.1	n.134+2957C>T		intron_variant	Intron 1 of 1	5
ENSG00000258654	ENST00000556397.1	n.245-6466C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 56180 AN: 132980 Hom.: 2114 Cov.: 98 FAILED QC

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.424

GnomAD4 exome AF: 0.402 AC: 1818 AN: 4526 Hom.: 93 Cov.: 0 AF XY: 0.400 AC XY: 1354 AN XY: 3384

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.316

Gnomad4 ASJ exome AF: 0.409

Gnomad4 EAS exome AF: 0.0705

Gnomad4 SAS exome AF: 0.336

Gnomad4 FIN exome AF: 0.445

Gnomad4 NFE exome AF: 0.422

Gnomad4 OTH exome AF: 0.371

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.422 AC: 56177 AN: 133062 Hom.: 2117 Cov.: 98 AF XY: 0.417 AC XY: 27037 AN XY: 64766

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.418

Alfa AF: 0.315 Hom.: 86

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1039353; hg19: chr15-20557661;