chr1-48084001-T-C

Variant names:

• chr1-48084001-T-C
• rs560004
• ENST00000635446.1:n.595T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02794	ENST00000635446.1	TSL:3	n.595T>C		non_coding_transcript_exon	Exon 5 of 6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.209 AC: 8688 AN: 41508

American (AMR) AF: 0.499 AC: 7623 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3470

East Asian (EAS) AF: 0.623 AC: 3219 AN: 5164

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4822

European-Finnish (FIN) AF: 0.379 AC: 3999 AN: 10556

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26156 AN: 67988

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.382 Hom.: 38918

Bravo AF: 0.358

Asia WGS AF: 0.502 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		0.55

Splicing

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

Other links and lift over

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