rs560004

Positions:

• chr1-48084001-T-C

Variant summary

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

The ENST00000635446.1(LINC02794):​n.595T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,106 control chromosomes in the GnomAD database, including 10,455 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 0.35 (10455 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC02794 ENST00000635446.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

Genes affected

LINC02794 (HGNC:54318): (long intergenic non-protein coding RNA 2794)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02794	XR_007066068.1	n.1483T>C		non_coding_transcript_exon_variant	5/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02794	ENST00000635446.1	n.595T>C		non_coding_transcript_exon_variant	5/6	3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53924 AN: 151986 Hom.: 10446 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.386

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.355 AC: 53935 AN: 152104 Hom.: 10455 Cov.: 32 AF XY: 0.361 AC XY: 26814 AN XY: 74338

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.390

Alfa AF: 0.392 Hom.: 25401

Bravo AF: 0.358

Asia WGS AF: 0.502 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs560004; hg19: chr1-48549673; COSMIC: COSV71692447;