ENST00000511634.2:n.467T>C

Variant names:

• chr4-54355782-T-C
• rs894905
• ENST00000511634.2:n.467T>C

Variant summary

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

The ENST00000511634.2(LINC02283):​n.467T>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 0.594 in 152,130 control chromosomes in the GnomAD database, including 27,835 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 0.59 (27832 hom., cov: 33)
  • Exomes 𝑓: 0.59 (3 hom.)
• Consequence: LINC02283 ENST00000511634.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06
• Publications: 7 publications found

Genes affected

LINC02283 (HGNC:53200): (long intergenic non-protein coding RNA 2283)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02283	NR_147160.1	n.302T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02283	ENST00000511634.2	n.467T>C		non_coding_transcript_exon_variant	Exon 2 of 2	3
LINC02283	ENST00000716476.1	n.273+23T>C		intron_variant	Intron 2 of 3
LINC02283	ENST00000801797.1	n.294+23T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90259 AN: 151990 Hom.: 27797 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.591 AC: 13 AN: 22 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.417 AC: 5 AN: 12

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.594 AC: 90353 AN: 152108 Hom.: 27832 Cov.: 33 AF XY: 0.599 AC XY: 44563 AN XY: 74348

African (AFR) AF: 0.755 AC: 31319 AN: 41498

American (AMR) AF: 0.559 AC: 8537 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1830 AN: 3468

East Asian (EAS) AF: 0.744 AC: 3855 AN: 5178

South Asian (SAS) AF: 0.674 AC: 3246 AN: 4818

European-Finnish (FIN) AF: 0.584 AC: 6165 AN: 10564

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33567 AN: 67984

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.536 Hom.: 12815

Bravo AF: 0.599

Asia WGS AF: 0.718 AC: 2495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs894905; hg19: chr4-55221949;