rs6632753

Variant names:

• chrX-13349952-C-T
• rs6632753
• ENST00000456091.2:n.614+12004C>T

Variant summary

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

The ENST00000456091.2(LINC01203):​n.614+12004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 111,157 control chromosomes in the GnomAD database, including 1,154 homozygotes. There are 3,324 hemizygotes in GnomAD. 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 0.11 (1154 hom., 3324 hem., cov: 22)
• Consequence: LINC01203 ENST00000456091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

LINC01203 (HGNC:49634): (long intergenic non-protein coding RNA 1203)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01203	ENST00000456091.2	n.614+12004C>T		intron_variant	Intron 5 of 10	3
LINC01203	ENST00000653729.1	n.139+12004C>T		intron_variant	Intron 2 of 7
LINC01203	ENST00000655502.1	n.512+12004C>T		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.110 AC: 12263 AN: 111103 Hom.: 1152 Cov.: 22 AF XY: 0.0990 AC XY: 3303 AN XY: 33347

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0131

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00169

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0420

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.111 AC: 12284 AN: 111157 Hom.: 1154 Cov.: 22 AF XY: 0.0995 AC XY: 3324 AN XY: 33411

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.00169

Gnomad4 SAS AF: 0.0136

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0245

Gnomad4 OTH AF: 0.0854

Alfa AF: 0.0530 Hom.: 1809

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6632753; hg19: chrX-13368071;