rs12191459

chr6-131946599-C-T

Variant summary

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

The ENST00000706294.1(LINC01013):n.182+44448C>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 0.126 in 152,150 control chromosomes in the GnomAD database, including 1,292 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 0.13 (1292 hom., cov: 33)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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+44448C>T		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+44448C>T		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+42365C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19094 AN: 152032 Hom.: 1292 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.126 AC: 19108 AN: 152150 Hom.: 1292 Cov.: 33 AF XY: 0.123 AC XY: 9118 AN XY: 74370

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0683

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.127

Alfa AF: 0.124 Hom.: 102

Bravo AF: 0.128

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.6
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12191459; hg19: chr6-132267739;