X-137531061-C-T

Variant names:

• chrX-137531061-C-T
• rs2746112
• ENST00000786828.1:n.219+155G>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+155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 111,049 control chromosomes in the GnomAD database, including 8,202 homozygotes. There are 15,150 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 0.45 (8202 hom., 15150 hem., cov: 23)
• Consequence: LINC02931 ENST00000786828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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+155G>A		intron	N/A
	LINC02931	ENST00000786829.1		n.244+155G>A		intron	N/A
	LINC02931	ENST00000786830.1		n.243+155G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 50085 AN: 110996 Hom.: 8200 Cov.: 23

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.451 AC: 50092 AN: 111049 Hom.: 8202 Cov.: 23 AF XY: 0.455 AC XY: 15150 AN XY: 33327

African (AFR) AF: 0.322 AC: 9884 AN: 30685

American (AMR) AF: 0.552 AC: 5747 AN: 10420

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1158 AN: 2624

East Asian (EAS) AF: 0.591 AC: 2083 AN: 3523

South Asian (SAS) AF: 0.554 AC: 1441 AN: 2599

European-Finnish (FIN) AF: 0.478 AC: 2824 AN: 5907

Middle Eastern (MID) AF: 0.372 AC: 80 AN: 215

European-Non Finnish (NFE) AF: 0.491 AC: 25962 AN: 52885

Other (OTH) AF: 0.458 AC: 695 AN: 1518

Alfa AF: 0.459 Hom.: 4264

Bravo AF: 0.449

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.69
PhyloP100		-0.42

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: rs2746112;

hg19: chrX-136613220;