rs4377733

Variant names:

• chr5-91280763-C-T
• rs4377733
• ENST00000440769.3:n.380G>A

Variant summary

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

The ENST00000660900.2(ENSG00000286638):​n.535C>T 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 0.829 in 152,318 control chromosomes in the GnomAD database, including 52,800 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 0.83 (52757 hom., cov: 33)
  • Exomes 𝑓: 0.94 (43 hom.)
• Consequence: ENSG00000286638 ENST00000660900.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

ENSG00000234292 (HGNC:):

LUCAT1 (HGNC:48498): (lung cancer associated transcript 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234292	ENST00000440769.3	n.380G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000286638	ENST00000660900.2	n.535C>T		non_coding_transcript_exon_variant	Exon 1 of 1
LUCAT1	ENST00000647807.1	n.463+32875G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126072 AN: 152102 Hom.: 52747 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.839

GnomAD4 exome AF: 0.939 AC: 92 AN: 98 Hom.: 43 Cov.: 0 AF XY: 0.919 AC XY: 57 AN XY: 62

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.978

Gnomad4 NFE exome AF: 0.977

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.829 AC: 126128 AN: 152220 Hom.: 52757 Cov.: 33 AF XY: 0.826 AC XY: 61491 AN XY: 74422

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.836

Alfa AF: 0.859 Hom.: 12105

Bravo AF: 0.816

Asia WGS AF: 0.667 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4377733; hg19: chr5-90576580;