ENST00000841293.1:n.773A>G

Variant names:

• chrX-13289612-A-G
• rs4830841
• ENST00000841293.1:n.773A>G

Variant summary

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

The ENST00000841293.1(ENSG00000309459):​n.773A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 111,056 control chromosomes in the GnomAD database, including 12,544 homozygotes. There are 17,423 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 0.53 (12544 hom., 17423 hem., cov: 23)
• Consequence: ENSG00000309459 ENST00000841293.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 0 publications found

Genes affected

ENSG00000309459 (HGNC:):

LINC02154 (HGNC:53015): (long intergenic non-protein coding RNA 2154)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841293.1. 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
	LINC02154	NR_146309.1		n.133+13708T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309459	ENST00000841293.1		n.773A>G		non_coding_transcript_exon	Exon 3 of 3
	LINC02154	ENST00000412485.3	TSL:2	n.95-2048T>C		intron	N/A
	LINC02154	ENST00000443965.1	TSL:2	n.133+13708T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 58336 AN: 111001 Hom.: 12525 Cov.: 23

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.526 AC: 58413 AN: 111056 Hom.: 12544 Cov.: 23 AF XY: 0.523 AC XY: 17423 AN XY: 33290

African (AFR) AF: 0.796 AC: 24267 AN: 30469

American (AMR) AF: 0.649 AC: 6814 AN: 10497

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 919 AN: 2642

East Asian (EAS) AF: 0.837 AC: 2970 AN: 3550

South Asian (SAS) AF: 0.561 AC: 1472 AN: 2626

European-Finnish (FIN) AF: 0.366 AC: 2153 AN: 5876

Middle Eastern (MID) AF: 0.364 AC: 78 AN: 214

European-Non Finnish (NFE) AF: 0.354 AC: 18787 AN: 52996

Other (OTH) AF: 0.528 AC: 796 AN: 1508

Alfa AF: 0.468 Hom.: 4490

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.44
DANN	Benign	0.38
PhyloP100		-0.20

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: rs4830841;

hg19: chrX-13307731;