8-53515506-G-A

Variant names:

• chr8-53515506-G-A
• rs7004273
• ENST00000426023.1:n.2052C>T

Variant summary

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

The ENST00000426023.1(LINC02984):​n.2052C>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 0.547 in 152,054 control chromosomes in the GnomAD database, including 22,944 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 0.55 (22942 hom., cov: 32)
  • Exomes 𝑓: 0.57 (2 hom.)
• Consequence: LINC02984 ENST00000426023.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 4 publications found

Genes affected

LINC02984 (HGNC:56063): (long intergenic non-protein coding RNA 2984)

ENSG00000254204 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426023.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02984	NR_149032.1		n.2086C>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02984	ENST00000426023.1	TSL:2	n.2052C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000254204	ENST00000521930.1	TSL:3	n.337G>A		non_coding_transcript_exon	Exon 1 of 2
	LINC02984	ENST00000656177.1		n.2457C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83156 AN: 151922 Hom.: 22948 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.571 AC: 8 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

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: 5 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.547 AC: 83188 AN: 152040 Hom.: 22942 Cov.: 32 AF XY: 0.549 AC XY: 40765 AN XY: 74312

African (AFR) AF: 0.495 AC: 20500 AN: 41454

American (AMR) AF: 0.534 AC: 8165 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2502 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3452 AN: 5160

South Asian (SAS) AF: 0.642 AC: 3085 AN: 4808

European-Finnish (FIN) AF: 0.563 AC: 5952 AN: 10580

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37828 AN: 67968

Other (OTH) AF: 0.570 AC: 1202 AN: 2110

Alfa AF: 0.548 Hom.: 12178

Bravo AF: 0.546

Asia WGS AF: 0.636 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs7004273; hg19: chr8-54428066;