rs1363364

Positions:

• chr19-34817436-A-T

Variant summary

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

The NR_033982.1(LINC01801):​n.798T>A 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 0.549 in 151,970 control chromosomes in the GnomAD database, including 23,655 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 0.55 (23646 hom., cov: 31)
  • Exomes 𝑓: 0.70 (9 hom.)
• Consequence: LINC01801 NR_033982.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.84

Genes affected

LINC01801 (HGNC:52592): (long intergenic non-protein coding RNA 1801)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01801	NR_033982.1	n.798T>A		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01801	ENST00000587150.3	n.180T>A		non_coding_transcript_exon_variant	2/5	5
LINC01801	ENST00000590963.1	n.798T>A		non_coding_transcript_exon_variant	6/6	1
LINC01801	ENST00000657681.1	n.701T>A		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83309 AN: 151808 Hom.: 23606 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.530

GnomAD4 exome AF: 0.705 AC: 31 AN: 44 Hom.: 9 Cov.: 0 AF XY: 0.694 AC XY: 25 AN XY: 36

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.684

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.549 AC: 83404 AN: 151926 Hom.: 23646 Cov.: 31 AF XY: 0.539 AC XY: 40053 AN XY: 74286

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.530

Alfa AF: 0.541 Hom.: 2864

Bravo AF: 0.558

Asia WGS AF: 0.438 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363364; hg19: chr19-35308340;