rs9493150

chr6-131952851-G-C

Variant summary

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

The ENST00000706336.1(LINC01013):n.86+1678G>C 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 0.299 in 152,034 control chromosomes in the GnomAD database, including 7,132 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 0.30 (7132 hom., cov: 32)
• Consequence: LINC01013 ENST00000706336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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	ENST00000706336.1	n.86+1678G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45429 AN: 151916 Hom.: 7121 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.299 AC: 45482 AN: 152034 Hom.: 7132 Cov.: 32 AF XY: 0.295 AC XY: 21937 AN XY: 74324

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.303

Alfa AF: 0.298 Hom.: 624

Bravo AF: 0.304

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.42
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9493150; hg19: chr6-132273991;