X-103552254-T-C

Variant names:

• chrX-103552254-T-C
• rs5987543
• ENST00000801435.1:n.705+2672A>G

Variant summary

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

The NR_131236.1(LINC02589):​n.378+2322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 111,290 control chromosomes in the GnomAD database, including 3,022 homozygotes. There are 8,414 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 0.25 (3022 hom., 8414 hem., cov: 23)
• Consequence: LINC02589 NR_131236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 2 publications found

Genes affected

ENSG00000287619 (HGNC:):

LINC02589 (HGNC:53859): (long intergenic non-protein coding RNA 2589)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_131236.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02589	NR_131236.1		n.378+2322A>G		intron	N/A
	LINC02589	NR_131237.1		n.28+2672A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287619	ENST00000801435.1		n.705+2672A>G		intron	N/A
	ENSG00000287619	ENST00000801437.1		n.33+2672A>G		intron	N/A
	ENSG00000287619	ENST00000801438.1		n.351+2322A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 28334 AN: 111236 Hom.: 3018 Cov.: 23

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.107

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.255 AC: 28356 AN: 111290 Hom.: 3022 Cov.: 23 AF XY: 0.251 AC XY: 8414 AN XY: 33534

African (AFR) AF: 0.366 AC: 11203 AN: 30606

American (AMR) AF: 0.358 AC: 3750 AN: 10467

Ashkenazi Jewish (ASJ) AF: 0.0984 AC: 259 AN: 2632

East Asian (EAS) AF: 0.432 AC: 1519 AN: 3518

South Asian (SAS) AF: 0.461 AC: 1215 AN: 2634

European-Finnish (FIN) AF: 0.177 AC: 1064 AN: 6001

Middle Eastern (MID) AF: 0.0991 AC: 21 AN: 212

European-Non Finnish (NFE) AF: 0.167 AC: 8869 AN: 53018

Other (OTH) AF: 0.218 AC: 332 AN: 1523

Alfa AF: 0.213 Hom.: 1692

Bravo AF: 0.276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.85
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs5987543; hg19: chrX-102807182;