8-53516436-T-C

Variant summary

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

The NR_149032.1(LINC02984):n.1156A>G 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 0.376 in 152,106 control chromosomes in the GnomAD database, including 13,007 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 0.38 (13004 hom., cov: 32)
  • Exomes 𝑓: 0.54 (3 hom.)
• Consequence: LINC02984 NR_149032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

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

LOC124901947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02984	NR_149032.1	n.1156A>G		non_coding_transcript_exon_variant	2/2
LOC124901947	XR_007060913.1	n.146-9196T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02984	ENST00000656976.1	n.879+276A>G		intron_variant, non_coding_transcript_variant
LINC02984	ENST00000426023.1	n.1122A>G		non_coding_transcript_exon_variant	2/2	2
LINC02984	ENST00000656177.1	n.1527A>G		non_coding_transcript_exon_variant	2/2
LINC02984	ENST00000670326.1	n.1168A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57259 AN: 151964 Hom.: 13011 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.417

GnomAD4 exome AF: 0.542 AC: 13 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 6 AN XY: 12

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.376 AC: 57252 AN: 152082 Hom.: 13004 Cov.: 32 AF XY: 0.371 AC XY: 27606 AN XY: 74328

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.415

Alfa AF: 0.490 Hom.: 37480

Bravo AF: 0.362

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.65
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504154; hg19: chr8-54428996;