chr6-131936884-T-C

Position:

• chr6-131936884-T-C

Variant summary

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

The ENST00000706294.1(LINC01013):​n.182+34733T>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 0.206 in 152,180 control chromosomes in the GnomAD database, including 3,787 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 0.21 (3787 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 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+34733T>C		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+34733T>C		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+32650T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31370 AN: 152062 Hom.: 3793 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.206 AC: 31375 AN: 152180 Hom.: 3787 Cov.: 32 AF XY: 0.213 AC XY: 15861 AN XY: 74390

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.226

Alfa AF: 0.206 Hom.: 864

Bravo AF: 0.198

Asia WGS AF: 0.375 AC: 1304 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12523697; hg19: chr6-132258024;