rs13114426

chr4-119801930-C-T

Variant summary

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

The NR_174111.1(LINC01365):n.235+794G>A 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 0.306 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 NR_174111.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01365	NR_174111.1	n.235+794G>A		intron_variant, non_coding_transcript_variant
LINC01365	NR_110660.2	n.236-536G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01365	ENST00000503266.6	n.273-536G>A		intron_variant, non_coding_transcript_variant		1
LINC01365	ENST00000512219.1	n.218+794G>A		intron_variant, non_coding_transcript_variant		5
LINC01365	ENST00000669300.1	n.235+794G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.289

Alfa AF: 0.335 Hom.: 1492

Bravo AF: 0.292

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13114426; hg19: chr4-120723085;