rs17246666

Variant names:

• chrX-17971150-G-A
• rs17246666
• ENST00000453902.1:n.475-720C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000453902.1(LINC01456):​n.475-720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0291 in 112,418 control chromosomes in the GnomAD database, including 40 homozygotes. There are 905 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 0.029 (40 hom., 905 hem., cov: 23)
• Consequence: LINC01456 ENST00000453902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 0 publications found

Genes affected

LINC01456 (HGNC:50846): (long intergenic non-protein coding RNA 1456)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0291 (3276/112418) while in subpopulation NFE AF = 0.0433 (2305/53271). AF 95% confidence interval is 0.0418. There are 40 homozygotes in GnomAd4. There are 905 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01456	NR_133641.1	n.475-720C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01456	ENST00000453902.1	n.475-720C>T		intron_variant	Intron 4 of 4	3
LINC01456	ENST00000844921.1	n.406-720C>T		intron_variant	Intron 3 of 6
LINC01456	ENST00000844922.1	n.160-26317C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0292 AC: 3278 AN: 112364 Hom.: 40 Cov.: 23

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0320

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00917

Gnomad FIN AF: 0.0213

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0257

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

GnomAD4 genome AF: 0.0291 AC: 3276 AN: 112418 Hom.: 40 Cov.: 23 AF XY: 0.0262 AC XY: 905 AN XY: 34578

African (AFR) AF: 0.0102 AC: 315 AN: 31018

American (AMR) AF: 0.0245 AC: 261 AN: 10633

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 163 AN: 2654

East Asian (EAS) AF: 0.00 AC: 0 AN: 3572

South Asian (SAS) AF: 0.00920 AC: 25 AN: 2718

European-Finnish (FIN) AF: 0.0213 AC: 130 AN: 6110

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.0433 AC: 2305 AN: 53271

Other (OTH) AF: 0.0254 AC: 39 AN: 1537

Alfa AF: 0.0328 Hom.: 239

Bravo AF: 0.0281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17246666; hg19: chrX-17989270;