X-17992789-G-T

Variant names:

• chrX-17992789-G-T
• rs17320692
• ENST00000453902.1:n.194+3000C>A

Variant summary

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

The ENST00000453902.1(LINC01456):​n.194+3000C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 110,913 control chromosomes in the GnomAD database, including 6,835 homozygotes. There are 8,487 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 0.27 (6835 hom., 8487 hem., cov: 22)
• Consequence: LINC01456 ENST00000453902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01456	NR_133641.1	n.194+3000C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01456	ENST00000453902.1	n.194+3000C>A		intron_variant	Intron 2 of 4	3
LINC01456	ENST00000844921.1	n.302-10195C>A		intron_variant	Intron 2 of 6
LINC01456	ENST00000844922.1	n.160-47956C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 29668 AN: 110863 Hom.: 6833 Cov.: 22

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.0102

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0743

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.268 AC: 29722 AN: 110913 Hom.: 6835 Cov.: 22 AF XY: 0.256 AC XY: 8487 AN XY: 33159

African (AFR) AF: 0.761 AC: 22992 AN: 30211

American (AMR) AF: 0.217 AC: 2274 AN: 10495

Ashkenazi Jewish (ASJ) AF: 0.0743 AC: 196 AN: 2637

East Asian (EAS) AF: 0.226 AC: 790 AN: 3494

South Asian (SAS) AF: 0.173 AC: 448 AN: 2596

European-Finnish (FIN) AF: 0.0779 AC: 469 AN: 6023

Middle Eastern (MID) AF: 0.137 AC: 29 AN: 212

European-Non Finnish (NFE) AF: 0.0404 AC: 2143 AN: 53039

Other (OTH) AF: 0.246 AC: 374 AN: 1520

Alfa AF: 0.177 Hom.: 1673

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs17320692; hg19: chrX-18010909;