rs9321315

Positions:

• chr6-131932136-A-T

Variant summary

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

The ENST00000706294.1(LINC01013):​n.182+29985A>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 0.103 in 151,682 control chromosomes in the GnomAD database, including 911 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 (911 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 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+29985A>T		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706326.1	n.239+29985A>T		intron_variant, non_coding_transcript_variant
LINC01013	ENST00000706327.1	n.559+27902A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15667 AN: 151564 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.103 AC: 15676 AN: 151682 Hom.: 911 Cov.: 32 AF XY: 0.106 AC XY: 7858 AN XY: 74122

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0951

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0998

Gnomad4 OTH AF: 0.107

Alfa AF: 0.105 Hom.: 107

Bravo AF: 0.0982

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.042
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321315; hg19: chr6-132253276;