20-6731216-T-C

Position:

• chr20-6731216-T-C

Variant summary

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

The NR_146909.1(LINC01713):​n.974A>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 0.539 in 151,988 control chromosomes in the GnomAD database, including 22,228 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 0.54 (22228 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC01713 NR_146909.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

LINC01713 (HGNC:52500): (long intergenic non-protein coding RNA 1713)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01713	NR_146909.1	n.974A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01713	ENST00000658541.1	n.692A>G		non_coding_transcript_exon_variant	3/3
LINC01713	ENST00000445589.1			downstream_gene_variant		3
LINC01713	ENST00000655019.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81828 AN: 151868 Hom.: 22206 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.539 AC: 81888 AN: 151986 Hom.: 22228 Cov.: 32 AF XY: 0.537 AC XY: 39851 AN XY: 74276

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.538

Alfa AF: 0.564 Hom.: 35638

Bravo AF: 0.538

Asia WGS AF: 0.438 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235713; hg19: chr20-6711863;