rs1931003

Positions:

• chr6-131944324-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+42173C>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 0.424 in 151,842 control chromosomes in the GnomAD database, including 13,663 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 0.42 (13663 hom., cov: 31)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

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 (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.1	n.182+42173C>T		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+42173C>T		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+40090C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64373 AN: 151722 Hom.: 13650 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.424 AC: 64424 AN: 151842 Hom.: 13663 Cov.: 31 AF XY: 0.421 AC XY: 31227 AN XY: 74210

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.418

Alfa AF: 0.429 Hom.: 2865

Bravo AF: 0.430

Asia WGS AF: 0.494 AC: 1718 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	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931003; hg19: chr6-132265464;