14-90489716-C-T

Position:

• chr14-90489716-C-T

Variant summary

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

The ENST00000666767.1(LINC00642):​n.323-17C>T variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,150 control chromosomes in the GnomAD database, including 26,000 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 0.57 (25996 hom., cov: 33)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: LINC00642 ENST00000666767.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

(HGNC:):

LINC00642 (HGNC:44293): (long intergenic non-protein coding RNA 642)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000647570.1	n.391G>A		non_coding_transcript_exon_variant	4/4
LINC00642	ENST00000666767.1	n.323-17C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87243 AN: 152002 Hom.: 25945 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.593

GnomAD4 exome AF: 0.500 AC: 15 AN: 30 Hom.: 4 Cov.: 0 AF XY: 0.455 AC XY: 10 AN XY: 22

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.574 AC: 87359 AN: 152120 Hom.: 25996 Cov.: 33 AF XY: 0.581 AC XY: 43172 AN XY: 74360

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.593

Alfa AF: 0.492 Hom.: 33542

Bravo AF: 0.591

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1294497; hg19: chr14-90956060;