rs4907792

Positions:

• chrX-51505931-C-T

Variant summary

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

The NR_110654.1(LINC01496):​n.218G>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 (17182 hom., 21905 hem., cov: 23)
  • Exomes 𝑓: 0.69 (2 hom. 7 hem.)
  • Failed GnomAD Quality Control
• Consequence: LINC01496 NR_110654.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01496	NR_110654.1	n.218G>A		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01496	ENST00000448761.1	n.97G>A		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 73258 AN: 110906 Hom.: 17184 Cov.: 23 AF XY: 0.661 AC XY: 21876 AN XY: 33116

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.668

GnomAD4 exome AF: 0.692 AC: 18 AN: 26 Hom.: 2 Cov.: 0 AF XY: 0.875 AC XY: 7 AN XY: 8

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.722

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.660 AC: 73280 AN: 110965 Hom.: 17182 Cov.: 23 AF XY: 0.660 AC XY: 21905 AN XY: 33185

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.672

Alfa AF: 0.647 Hom.: 9298

Bravo AF: 0.680

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4907792; hg19: chrX-51248783;