6-131960724-C-T

Position:

• chr6-131960724-C-T

Variant summary

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

The ENST00000706336.1(LINC01013):​n.86+9551C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,964 control chromosomes in the GnomAD database, including 2,551 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 0.16 (2551 hom., cov: 31)
• Consequence: LINC01013 ENST00000706336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706336.1	n.86+9551C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24761 AN: 151846 Hom.: 2550 Cov.: 31

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.163 AC: 24776 AN: 151964 Hom.: 2551 Cov.: 31 AF XY: 0.166 AC XY: 12359 AN XY: 74260

Gnomad4 AFR AF: 0.0492

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.167

Alfa AF: 0.168 Hom.: 274

Bravo AF: 0.157

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10872386; hg19: chr6-132281864;