rs7141809

chr14-50094227-A-G

Variant summary

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

The NR_131171.1(LINC01599):n.48-5032T>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 0.301 in 152,056 control chromosomes in the GnomAD database, including 7,929 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 0.30 (7929 hom., cov: 32)
• Consequence: LINC01599 NR_131171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

LINC01599 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01599	NR_131171.1	n.48-5032T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01588	ENST00000603228.3	n.107-5032T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45666 AN: 151938 Hom.: 7927 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.301 AC: 45694 AN: 152056 Hom.: 7929 Cov.: 32 AF XY: 0.298 AC XY: 22140 AN XY: 74320

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.316

Alfa AF: 0.371 Hom.: 5480

Bravo AF: 0.282

Asia WGS AF: 0.248 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	19
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7141809; hg19: chr14-50560945;