X-51505931-C-T

Variant names:

• chrX-51505931-C-T
• rs4907792
• ENST00000448761.2:n.295G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448761.2(LINC01496):​n.295G>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 ENST00000448761.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01496	NR_110654.1	n.218G>A		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01496	ENST00000448761.2	n.295G>A		non_coding_transcript_exon_variant	Exon 2 of 4	5
LINC01496	ENST00000827922.1	n.274G>A		non_coding_transcript_exon_variant	Exon 2 of 4
LINC01496	ENST00000827923.1	n.263G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

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

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.722 AC: 13 AN: 18

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.640 AC: 19526 AN: 30531

American (AMR) AF: 0.784 AC: 8161 AN: 10408

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 1976 AN: 2637

East Asian (EAS) AF: 0.924 AC: 3209 AN: 3472

South Asian (SAS) AF: 0.717 AC: 1890 AN: 2636

European-Finnish (FIN) AF: 0.560 AC: 3346 AN: 5972

Middle Eastern (MID) AF: 0.668 AC: 143 AN: 214

European-Non Finnish (NFE) AF: 0.635 AC: 33617 AN: 52900

Other (OTH) AF: 0.672 AC: 1019 AN: 1516

Alfa AF: 0.641 Hom.: 16472

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4907792; hg19: chrX-51248783;