X-13349952-C-T

Position:

• chrX-13349952-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.13349952C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01203	ENST00000456091.2	n.614+12004C>T		intron_variant		3
LINC01203	ENST00000653729.1	n.139+12004C>T		intron_variant
LINC01203	ENST00000655502.1	n.512+12004C>T		intron_variant

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;