20-44659446-C-T

Variant summary

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

The NR_034104.1(LINC01260):n.369+265G>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 0.582 in 152,046 control chromosomes in the GnomAD database, including 27,183 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 0.58 (27183 hom., cov: 32)
• Consequence: LINC01260 NR_034104.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

LINC01260 (HGNC:49900): (long intergenic non-protein coding RNA 1260)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01260	NR_034104.1	n.369+265G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01260	ENST00000255183.8	n.213+265G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88446 AN: 151928 Hom.: 27182 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.582 AC: 88481 AN: 152046 Hom.: 27183 Cov.: 32 AF XY: 0.587 AC XY: 43657 AN XY: 74312

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.609

Alfa AF: 0.655 Hom.: 59447

Bravo AF: 0.560

Asia WGS AF: 0.617 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6094017; hg19: chr20-43288087;