rs13114426

Variant names:

• chr4-119801930-C-T
• rs13114426
• ENST00000503266.6:n.273-536G>A

Variant summary

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

The ENST00000503266.6(LINC01365):​n.273-536G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,944 control chromosomes in the GnomAD database, including 8,084 homozygotes. 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 0.31 (8084 hom., cov: 31)
• Consequence: LINC01365 ENST00000503266.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 3 publications found

Genes affected

LINC01365 (HGNC:50603): (long intergenic non-protein coding RNA 1365)

ENSG00000300267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503266.6. 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
	LINC01365	NR_110660.2		n.236-536G>A		intron	N/A
	LINC01365	NR_174111.1		n.235+794G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01365	ENST00000503266.6	TSL:1	n.273-536G>A		intron	N/A
	LINC01365	ENST00000512219.1	TSL:5	n.218+794G>A		intron	N/A
	LINC01365	ENST00000669300.2		n.239+794G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46451 AN: 151826 Hom.: 8084 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.306 AC: 46452 AN: 151944 Hom.: 8084 Cov.: 31 AF XY: 0.304 AC XY: 22588 AN XY: 74256

African (AFR) AF: 0.137 AC: 5679 AN: 41452

American (AMR) AF: 0.281 AC: 4291 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1725 AN: 5148

South Asian (SAS) AF: 0.244 AC: 1173 AN: 4808

European-Finnish (FIN) AF: 0.373 AC: 3932 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27162 AN: 67944

Other (OTH) AF: 0.289 AC: 611 AN: 2112

Alfa AF: 0.329 Hom.: 1498

Bravo AF: 0.292

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.73
PhyloP100		-0.079

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: rs13114426;

hg19: chr4-120723085;