5-91268322-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647807.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUCAT1	ENST00000647807.1		n.464-23312G>A		intron	N/A
	LUCAT1	ENST00000648385.1		n.367+45316G>A		intron	N/A
	LUCAT1	ENST00000648822.1		n.437-3609G>A		intron	N/A

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

African (AFR) AF: 0.664 AC: 26613 AN: 40074

American (AMR) AF: 0.744 AC: 10967 AN: 14738

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3149 AN: 3462

East Asian (EAS) AF: 0.536 AC: 2725 AN: 5086

South Asian (SAS) AF: 0.752 AC: 3580 AN: 4762

European-Finnish (FIN) AF: 0.894 AC: 8258 AN: 9238

Middle Eastern (MID) AF: 0.821 AC: 230 AN: 280

European-Non Finnish (NFE) AF: 0.877 AC: 59271 AN: 67606

Other (OTH) AF: 0.810 AC: 1669 AN: 2060

Alfa AF: 0.827 Hom.: 6820

Bravo AF: 0.773

Asia WGS AF: 0.657 AC: 2286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.4
DANN	Benign	0.77
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10474346; hg19: chr5-90564139;