4-54375414-C-T

Variant names:

• chr4-54375414-C-T
• rs9312648
• ENST00000801800.1:n.603C>T

Variant summary

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

The ENST00000801800.1(LINC02283):​n.603C>T 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 0.386 in 152,040 control chromosomes in the GnomAD database, including 11,705 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 0.39 (11705 hom., cov: 32)
• Consequence: LINC02283 ENST00000801800.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02283	ENST00000801800.1	n.603C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02283	ENST00000801801.1	n.1428C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LINC02283	ENST00000801802.1	n.1044C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58646 AN: 151922 Hom.: 11686 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.386 AC: 58707 AN: 152040 Hom.: 11705 Cov.: 32 AF XY: 0.380 AC XY: 28228 AN XY: 74306

African (AFR) AF: 0.472 AC: 19567 AN: 41458

American (AMR) AF: 0.382 AC: 5838 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5162

South Asian (SAS) AF: 0.240 AC: 1158 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3335 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25438 AN: 67972

Other (OTH) AF: 0.399 AC: 842 AN: 2112

Alfa AF: 0.403 Hom.: 6446

Bravo AF: 0.395

Asia WGS AF: 0.234 AC: 815 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	0.27
DANN	Benign	0.68
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9312648; hg19: chr4-55241581;