X-137515426-C-T

Variant names:

• chrX-137515426-C-T
• rs2859253
• ENST00000786828.1:n.219+15790G>A

Variant summary

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

The ENST00000786828.1(LINC02931):​n.219+15790G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 110,479 control chromosomes in the GnomAD database, including 5,131 homozygotes. There are 10,551 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 0.34 (5131 hom., 10551 hem., cov: 22)
• Consequence: LINC02931 ENST00000786828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 1 publications found

Genes affected

LINC02931 (HGNC:55853): (long intergenic non-protein coding RNA 2931)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786828.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02931	ENST00000786828.1		n.219+15790G>A		intron	N/A
	LINC02931	ENST00000786829.1		n.244+15790G>A		intron	N/A
	LINC02931	ENST00000786830.1		n.243+15790G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 37953 AN: 110426 Hom.: 5131 Cov.: 22

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.344 AC: 37960 AN: 110479 Hom.: 5131 Cov.: 22 AF XY: 0.322 AC XY: 10551 AN XY: 32773

African (AFR) AF: 0.480 AC: 14542 AN: 30315

American (AMR) AF: 0.251 AC: 2616 AN: 10406

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 883 AN: 2635

East Asian (EAS) AF: 0.343 AC: 1183 AN: 3450

South Asian (SAS) AF: 0.245 AC: 633 AN: 2586

European-Finnish (FIN) AF: 0.233 AC: 1375 AN: 5912

Middle Eastern (MID) AF: 0.379 AC: 81 AN: 214

European-Non Finnish (NFE) AF: 0.302 AC: 15954 AN: 52784

Other (OTH) AF: 0.318 AC: 479 AN: 1508

Alfa AF: 0.326 Hom.: 2296

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.78
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2859253;

hg19: chrX-136597585;