rs6117401

Variant names:

• chr20-6735450-G-A
• rs6117401
• ENST00000742970.1:n.177C>T

Variant summary

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

The ENST00000742970.1(LINC01713):​n.177C>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 0.33 in 152,038 control chromosomes in the GnomAD database, including 9,574 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 0.33 (9574 hom., cov: 32)
• Consequence: LINC01713 ENST00000742970.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742970.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01713	NR_146909.1		n.361-326C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01713	ENST00000742970.1		n.177C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01713	ENST00000445589.1	TSL:3	n.361-326C>T		intron	N/A
	LINC01713	ENST00000655019.1		n.99+778C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50108 AN: 151918 Hom.: 9567 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.335

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.330 AC: 50130 AN: 152038 Hom.: 9574 Cov.: 32 AF XY: 0.332 AC XY: 24661 AN XY: 74328

African (AFR) AF: 0.135 AC: 5611 AN: 41482

American (AMR) AF: 0.410 AC: 6267 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1126 AN: 5148

South Asian (SAS) AF: 0.464 AC: 2237 AN: 4818

European-Finnish (FIN) AF: 0.376 AC: 3972 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28432 AN: 67962

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.387 Hom.: 47453

Bravo AF: 0.321

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.31
DANN	Benign	0.68
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6117401;

hg19: chr20-6716097;