5-91260741-C-T

Variant summary

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

The ENST00000650150.1(LUCAT1):n.379+52897G>A 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 0.8 in 152,114 control chromosomes in the GnomAD database, including 49,462 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 0.80 (49462 hom., cov: 31)
• Consequence: LUCAT1 ENST00000650150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

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

LOC107986432 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986432	XR_001742795.2	n.611+3922G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LUCAT1	ENST00000650150.1	n.379+52897G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121680 AN: 151996 Hom.: 49433 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.800 AC: 121759 AN: 152114 Hom.: 49462 Cov.: 31 AF XY: 0.799 AC XY: 59421 AN XY: 74354

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.812

Alfa AF: 0.856 Hom.: 72527

Bravo AF: 0.784

Asia WGS AF: 0.665 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.31
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1858309; hg19: chr5-90556558;