rs9803659

chr1-167187263-T-C

Variant summary

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

The NR_110811.1(LINC01363):n.249-5070A>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 0.357 in 152,000 control chromosomes in the GnomAD database, including 9,919 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 0.36 (9919 hom., cov: 32)
• Consequence: LINC01363 NR_110811.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

Genes affected

LINC01363 (HGNC:50598): (long intergenic non-protein coding RNA 1363)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01363	NR_110811.1	n.249-5070A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01363	ENST00000446687.1	n.236-5070A>G		intron_variant, non_coding_transcript_variant		1
LINC01363	ENST00000457941.6	n.160-5070A>G		intron_variant, non_coding_transcript_variant		5
LINC01363	ENST00000426709.5	n.201-5070A>G		intron_variant, non_coding_transcript_variant		5
LINC01363	ENST00000428030.5	n.188+7795A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54288 AN: 151882 Hom.: 9908 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.357 AC: 54332 AN: 152000 Hom.: 9919 Cov.: 32 AF XY: 0.354 AC XY: 26324 AN XY: 74316

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.349

Alfa AF: 0.369 Hom.: 24302

Bravo AF: 0.360

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9803659; hg19: chr1-167156500;