rs928505

Positions:

• chr6-131977001-G-A
• chr6-131977001-G-C
• chr6-131977001-G-T

Variant summary

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

The ENST00000706336.1(LINC01013):​n.86+25828G>A 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 0.425 in 151,948 control chromosomes in the GnomAD database, including 14,722 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 0.42 (14722 hom., cov: 32)
• Consequence: LINC01013 ENST00000706336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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+25828G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64466 AN: 151830 Hom.: 14703 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.425 AC: 64517 AN: 151948 Hom.: 14722 Cov.: 32 AF XY: 0.434 AC XY: 32234 AN XY: 74260

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.455

Alfa AF: 0.446 Hom.: 31884

Bravo AF: 0.420

Asia WGS AF: 0.659 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928505; hg19: chr6-132298141;