rs2375990

chr4-36611742-C-Gchr4-36611742-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.124+3712G>C 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 0.846 in 151,978 control chromosomes in the GnomAD database, including 54,570 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 0.85 (54570 hom., cov: 30)
• Consequence: LINC02505 NR_149124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02505	NR_149124.1	n.124+3712G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02505	ENST00000510597.6	n.135+3712G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128405 AN: 151860 Hom.: 54530 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.846 AC: 128502 AN: 151978 Hom.: 54570 Cov.: 30 AF XY: 0.846 AC XY: 62797 AN XY: 74270

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.863

Alfa AF: 0.854 Hom.: 6508

Bravo AF: 0.840

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2375990; hg19: chr4-36613364;