chrX-51498820-C-T

Variant names:

• chrX-51498820-C-T
• rs5945619
• ENST00000656579.1:n.1346G>A

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 119 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656579.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01496	ENST00000656579.1		n.1346G>A		non_coding_transcript_exon	Exon 3 of 3
	LINC01496	ENST00000827922.1		n.*240G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.657 AC: 72368 AN: 110204 Hom.: 16965 Cov.: 22

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

African (AFR) AF: 0.623 AC: 18865 AN: 30299

American (AMR) AF: 0.785 AC: 8195 AN: 10442

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 1973 AN: 2638

East Asian (EAS) AF: 0.922 AC: 3197 AN: 3466

South Asian (SAS) AF: 0.722 AC: 1801 AN: 2496

European-Finnish (FIN) AF: 0.564 AC: 3307 AN: 5860

Middle Eastern (MID) AF: 0.665 AC: 141 AN: 212

European-Non Finnish (NFE) AF: 0.636 AC: 33500 AN: 52668

Other (OTH) AF: 0.674 AC: 1017 AN: 1510

Alfa AF: 0.646 Hom.: 65996

Bravo AF: 0.674

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.94
DANN	Benign	0.43
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs5945619; hg19: chrX-51241672;