chr6-131961884-G-A

Position:

• chr6-131961884-G-A

Variant summary

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

The ENST00000706336.1(LINC01013):​n.86+10711G>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 0.905 in 152,138 control chromosomes in the GnomAD database, including 62,393 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 0.91 (62393 hom., cov: 31)
• Consequence: LINC01013 ENST00000706336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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+10711G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137642 AN: 152020 Hom.: 62340 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.898

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.905 AC: 137752 AN: 152138 Hom.: 62393 Cov.: 31 AF XY: 0.907 AC XY: 67486 AN XY: 74368

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.919

Alfa AF: 0.895 Hom.: 7575

Bravo AF: 0.908

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2327184; hg19: chr6-132283024;