rs17749927

Positions:

• chr6-27702197-A-G

Variant summary

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

The NR_038294.1(LINC01012):​n.473-117A>G 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 0.0535 in 152,230 control chromosomes in the GnomAD database, including 336 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 0.054 (336 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01012 NR_038294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

LINC01012 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01012	NR_038294.1	n.473-117A>G		intron_variant, non_coding_transcript_variant
LINC01012	NR_038292.1	n.149-117A>G		intron_variant, non_coding_transcript_variant
LINC01012	NR_038293.1	n.473-117A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01012	ENST00000693645.1	n.481-117A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8153 AN: 152112 Hom.: 336 Cov.: 31

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0421

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.0535 AC: 8150 AN: 152230 Hom.: 336 Cov.: 31 AF XY: 0.0483 AC XY: 3597 AN XY: 74450

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0357

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0387

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0760 Hom.: 698

Bravo AF: 0.0525

Asia WGS AF: 0.00433 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17749927; hg19: chr6-27669976;