rs6926879

chr6-131941221-C-Achr6-131941221-C-G

Variant summary

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

The ENST00000706294.1(LINC01013):n.182+39070C>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 0.409 in 151,960 control chromosomes in the GnomAD database, including 13,229 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 0.41 (13229 hom., cov: 30)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 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+39070C>A		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+39070C>A		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+36987C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62169 AN: 151842 Hom.: 13225 Cov.: 30

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.409 AC: 62188 AN: 151960 Hom.: 13229 Cov.: 30 AF XY: 0.406 AC XY: 30159 AN XY: 74252

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.412

Alfa AF: 0.308 Hom.: 842

Bravo AF: 0.403

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6926879; hg19: chr6-132262361;