rs3037970

Positions:

• chr6-131954052-T-TTAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000706336.1(LINC01013):​n.86+2880_86+2884dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (22555 hom., cov: 0)
• Consequence: LINC01013 ENST00000706336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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+2880_86+2884dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81270 AN: 151176 Hom.: 22512 Cov.: 0

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.538 AC: 81367 AN: 151296 Hom.: 22555 Cov.: 0 AF XY: 0.535 AC XY: 39540 AN XY: 73896

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.529

Alfa AF: 0.528 Hom.: 1666

Asia WGS AF: 0.560 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3037970; hg19: chr6-132275192;