15-20352408-C-T

Position:

• chr15-20352408-C-T

Variant summary

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

The ENST00000556397.1(ENSG00000258654):​n.245-6466C>T variant causes a intron, non coding transcript 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: ENST00000556397.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556397.1	n.245-6466C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000557528.1	n.48C>T		non_coding_transcript_exon_variant	1/2	5
	ENST00000554815.1	n.134+2957C>T		intron_variant, non_coding_transcript_variant		5

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;