rs8013833

chr14-50047635-G-Achr14-50047635-G-Cchr14-50047635-G-T

Variant summary

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

The NR_131171.1(LINC01599):n.254-46C>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 0.0312 in 152,600 control chromosomes in the GnomAD database, including 142 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 0.031 (142 hom., cov: 30)
  • Exomes 𝑓: 0.0029 (0 hom.)
• Consequence: LINC01599 NR_131171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

LINC01588 (HGNC:27503): (long intergenic non-protein coding RNA 1588)

LINC01599 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01599	NR_131171.1	n.254-46C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01588	ENST00000635379.1	n.215-46C>T		intron_variant, non_coding_transcript_variant		5
LINC01588	ENST00000556019.2	n.187-46C>T		intron_variant, non_coding_transcript_variant		3
LINC01588	ENST00000557142.6	n.2566+5139C>T		intron_variant, non_coding_transcript_variant		3
LINC01588	ENST00000603228.3	n.313-46C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0313 AC: 4757 AN: 152138 Hom.: 142 Cov.: 30

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0336

GnomAD4 exome AF: 0.00291 AC: 1 AN: 344 Hom.: 0 Cov.: 0 AF XY: 0.00420 AC XY: 1 AN XY: 238

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00385

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0313 AC: 4763 AN: 152256 Hom.: 142 Cov.: 30 AF XY: 0.0301 AC XY: 2238 AN XY: 74452

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.0187

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00601

Gnomad4 FIN AF: 0.00603

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.0332

Alfa AF: 0.00937 Hom.: 3

Bravo AF: 0.0344

Asia WGS AF: 0.00982 AC: 35 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	3.8
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: rs8013833; hg19: chr14-50514353;