X-13356837-C-T

Position:

• chrX-13356837-C-T

Variant summary

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

The ENST00000661545.1(LINC01203):​n.1110-15412C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 108,982 control chromosomes in the GnomAD database, including 12,915 homozygotes. There are 16,382 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 0.53 (12915 hom., 16382 hem., cov: 21)
• Consequence: LINC01203 ENST00000661545.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01203	ENST00000661545.1	n.1110-15412C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.525 AC: 57193 AN: 108928 Hom.: 12895 Cov.: 21 AF XY: 0.522 AC XY: 16318 AN XY: 31280

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.526 AC: 57274 AN: 108982 Hom.: 12915 Cov.: 21 AF XY: 0.523 AC XY: 16382 AN XY: 31344

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.532

Alfa AF: 0.425 Hom.: 3104

Bravo AF: 0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.61
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4830495; hg19: chrX-13374956;