ENST00000658541.1:n.692A>G

Variant names:

• chr20-6731216-T-C
• rs235713
• ENST00000658541.1:n.692A>G

Variant summary

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

The ENST00000658541.1(LINC01713):​n.692A>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 ENST00000658541.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658541.1. 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
	LINC01713	NR_146909.1		n.974A>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01713	ENST00000658541.1		n.692A>G		non_coding_transcript_exon	Exon 3 of 3
	LINC01713	ENST00000445589.1	TSL:3	n.*42A>G		downstream_gene	N/A
	LINC01713	ENST00000655019.1		n.*28A>G		downstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

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: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.522 AC: 21639 AN: 41442

American (AMR) AF: 0.546 AC: 8337 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1459 AN: 5166

South Asian (SAS) AF: 0.579 AC: 2787 AN: 4816

European-Finnish (FIN) AF: 0.513 AC: 5411 AN: 10540

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38359 AN: 67980

Other (OTH) AF: 0.538 AC: 1129 AN: 2100

Alfa AF: 0.560 Hom.: 53954

Bravo AF: 0.538

Asia WGS AF: 0.438 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.57
PhyloP100		-0.024
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs235713; hg19: chr20-6711863;