rs1347190

Positions:

• chr13-99995845-A-G
• chr13-99995845-A-T

Variant summary

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

The NR_047483.1(LINC00554):​n.2065T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,150 control chromosomes in the GnomAD database, including 10,372 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 (10372 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC00554 NR_047483.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

Genes affected

LINC00554 (HGNC:43697): (long intergenic non-protein coding RNA 554)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00554	NR_047483.1	n.2065T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00554	ENST00000564841.1	n.2065T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54270 AN: 152026 Hom.: 10371 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.357 AC: 54293 AN: 152146 Hom.: 10372 Cov.: 33 AF XY: 0.351 AC XY: 26141 AN XY: 74372

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.400

Alfa AF: 0.425 Hom.: 16701

Bravo AF: 0.354

Asia WGS AF: 0.234 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347190; hg19: chr13-100648099;