4-36526231-C-T

Variant names:

• chr4-36526231-C-T
• rs2375971
• ENST00000505298.5:n.367-27743G>A

Variant summary

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

The ENST00000505298.5(LINC02505):​n.367-27743G>A variant causes a intron 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 ENST00000505298.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 publications found

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02505	NR_149124.1	n.199-27743G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02505	ENST00000505298.5	n.367-27743G>A		intron_variant	Intron 4 of 5	5
LINC02505	ENST00000510597.7	n.218-27743G>A		intron_variant	Intron 3 of 4	3
LINC02505	ENST00000662117.2	n.246-27743G>A		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.410 AC: 16942 AN: 41328

American (AMR) AF: 0.384 AC: 5862 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3464

East Asian (EAS) AF: 0.434 AC: 2242 AN: 5162

South Asian (SAS) AF: 0.449 AC: 2158 AN: 4804

European-Finnish (FIN) AF: 0.516 AC: 5386 AN: 10444

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28918 AN: 67870

Other (OTH) AF: 0.386 AC: 813 AN: 2104

Alfa AF: 0.413 Hom.: 37914

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2375971; hg19: chr4-36527853;