X-103552254-T-C

Position:

• chrX-103552254-T-C

Variant summary

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

The NR_131237.1(LINC02589):​n.28+2672A>G variant causes a intron, non coding transcript 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_131237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

Genes affected

LINC02589 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02589	NR_131237.1	n.28+2672A>G		intron_variant, non_coding_transcript_variant
LINC02589	NR_131236.1	n.378+2322A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 28334 AN: 111236 Hom.: 3018 Cov.: 23 AF XY: 0.251 AC XY: 8399 AN XY: 33470

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

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.0984

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.218

Alfa AF: 0.213 Hom.: 1692

Bravo AF: 0.276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5987543; hg19: chrX-102807182;