5-91268322-C-T

Variant names:

• chr5-91268322-C-T
• rs10474346
• ENST00000647807.1:n.464-23312G>A

Variant summary

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

The ENST00000647807.1(LUCAT1):​n.464-23312G>A variant causes a intron 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 ENST00000647807.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUCAT1	ENST00000647807.1	n.464-23312G>A		intron_variant	Intron 2 of 6
LUCAT1	ENST00000648385.1	n.367+45316G>A		intron_variant	Intron 2 of 5
LUCAT1	ENST00000648822.1	n.437-3609G>A		intron_variant	Intron 2 of 5

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;