X-13356837-C-T

Variant names:

• chrX-13356837-C-T
• rs4830495
• ENST00000456091.2:n.615-15412C>T

Variant summary

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

The ENST00000456091.2(LINC01203):​n.615-15412C>T variant causes a intron 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 ENST00000456091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456091.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01203	ENST00000456091.2	TSL:3	n.615-15412C>T		intron	N/A
	LINC01203	ENST00000653729.1		n.140-15531C>T		intron	N/A
	LINC01203	ENST00000655502.1		n.513-15412C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 57193 AN: 108928 Hom.: 12895 Cov.: 21

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

African (AFR) AF: 0.834 AC: 24952 AN: 29914

American (AMR) AF: 0.654 AC: 6692 AN: 10239

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 897 AN: 2612

East Asian (EAS) AF: 0.836 AC: 2845 AN: 3404

South Asian (SAS) AF: 0.515 AC: 1299 AN: 2521

European-Finnish (FIN) AF: 0.355 AC: 1957 AN: 5512

Middle Eastern (MID) AF: 0.358 AC: 76 AN: 212

European-Non Finnish (NFE) AF: 0.336 AC: 17603 AN: 52409

Other (OTH) AF: 0.532 AC: 796 AN: 1497

Alfa AF: 0.425 Hom.: 3104

Bravo AF: 0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.61
DANN	Benign	0.82
PhyloP100		0.026

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4830495;

hg19: chrX-13374956;