rs2375971

chr4-36526231-C-T

Variant summary

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

The NR_149124.1(LINC02505):n.199-27743G>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 0.423 in 151,630 control chromosomes in the GnomAD database, including 13,619 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 0.42 (13619 hom., cov: 31)
• Consequence: LINC02505 NR_149124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

Genes affected

LINC02505 (HGNC:53494): (long intergenic non-protein coding RNA 2505)

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 (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02505	NR_149124.1	n.199-27743G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02505	ENST00000510597.6	n.210-27743G>A		intron_variant, non_coding_transcript_variant		3
LINC02505	ENST00000505298.5	n.367-27743G>A		intron_variant, non_coding_transcript_variant		5
LINC02505	ENST00000662117.1	n.233-27743G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64115 AN: 151512 Hom.: 13623 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.423 AC: 64145 AN: 151630 Hom.: 13619 Cov.: 31 AF XY: 0.429 AC XY: 31763 AN XY: 74114

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.386

Alfa AF: 0.410 Hom.: 17143

Bravo AF: 0.408

Asia WGS AF: 0.429 AC: 1489 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2375971; hg19: chr4-36527853;