X-51498820-C-T

Position:

• chrX-51498820-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000656579.1(LINC01496):​n.1346G>A 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 0.66 (16963 hom., 21374 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: LINC01496 ENST00000656579.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

Genes affected

LINC01496 (HGNC:51162): (long intergenic non-protein coding RNA 1496)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01496	ENST00000656579.1	n.1346G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.657 AC: 72368 AN: 110204 Hom.: 16965 Cov.: 22 AF XY: 0.658 AC XY: 21352 AN XY: 32460

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.670

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.656 AC: 72383 AN: 110256 Hom.: 16963 Cov.: 22 AF XY: 0.657 AC XY: 21374 AN XY: 32522

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.674

Alfa AF: 0.645 Hom.: 38042

Bravo AF: 0.674

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.94
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945619; hg19: chrX-51241672;