rs6917644

chr6-131944525-A-G

Variant summary

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

The ENST00000706294.1(LINC01013):n.182+42374A>G 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 0.103 in 152,156 control chromosomes in the GnomAD database, including 895 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 0.10 (895 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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+42374A>G		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+42374A>G		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+40291A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15673 AN: 152038 Hom.: 896 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.103 AC: 15682 AN: 152156 Hom.: 895 Cov.: 32 AF XY: 0.0998 AC XY: 7424 AN XY: 74408

Gnomad4 AFR AF: 0.0724

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0676

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.114

Alfa AF: 0.115 Hom.: 360

Bravo AF: 0.102

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.3
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6917644; hg19: chr6-132265665;