5-91268322-C-T

Position:

• chr5-91268322-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+45316G>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 0.791 in 148,204 control chromosomes in the GnomAD database, including 47,330 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 0.79 (47330 hom., cov: 25)
• Consequence: LUCAT1 ENST00000650150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

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=-0.7).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LUCAT1	ENST00000650150.1	n.379+45316G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.791 AC: 117236 AN: 148128 Hom.: 47318 Cov.: 25

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.791 AC: 117278 AN: 148204 Hom.: 47330 Cov.: 25 AF XY: 0.789 AC XY: 56803 AN XY: 71952

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.810

Alfa AF: 0.835 Hom.: 6674

Bravo AF: 0.773

Asia WGS AF: 0.657 AC: 2286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10474346; hg19: chr5-90564139;