rs9493149

chr6-131937619-G-A

Variant summary

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

The ENST00000706294.1(LINC01013):n.182+35468G>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 0.195 in 152,050 control chromosomes in the GnomAD database, including 3,494 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 0.19 (3494 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01013	ENST00000706294.1	n.182+35468G>A		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+35468G>A		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+33385G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29615 AN: 151932 Hom.: 3497 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.195 AC: 29618 AN: 152050 Hom.: 3494 Cov.: 32 AF XY: 0.203 AC XY: 15062 AN XY: 74324

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.219

Alfa AF: 0.215 Hom.: 1867

Bravo AF: 0.185

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.62
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9493149; hg19: chr6-132258759;