rs7004273

Positions:

• chr8-53515506-G-A
• chr8-53515506-G-C

Variant summary

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

The NR_149032.1(LINC02984):​n.2086C>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 NR_149032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02984	NR_149032.1	n.2086C>T		non_coding_transcript_exon_variant	2/2
LOC124901947	XR_007060913.1	n.146-10126G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000521930.1	n.337G>A		non_coding_transcript_exon_variant	1/2	3
LINC02984	ENST00000656976.1	n.879+1206C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 EAS exome AF: 0.750

Gnomad4 NFE exome AF: 0.500

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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.570

Alfa AF: 0.548 Hom.: 7131

Bravo AF: 0.546

Asia WGS AF: 0.636 AC: 2214 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	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7004273; hg19: chr8-54428066;