chr5-91260741-C-T

Variant names:

• chr5-91260741-C-T
• rs1858309
• ENST00000647807.1:n.464-15731G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647807.1(LUCAT1):​n.464-15731G>A variant causes a intron 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 ENST00000647807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 3 publications found

Genes affected

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

LOC107986432 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.464-15731G>A		intron	N/A
	LUCAT1	ENST00000648385.1		n.367+52897G>A		intron	N/A
	LUCAT1	ENST00000648822.1		n.487+3922G>A		intron	N/A

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

African (AFR) AF: 0.702 AC: 29105 AN: 41470

American (AMR) AF: 0.748 AC: 11419 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3153 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2835 AN: 5170

South Asian (SAS) AF: 0.752 AC: 3618 AN: 4812

European-Finnish (FIN) AF: 0.889 AC: 9413 AN: 10592

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59436 AN: 68008

Other (OTH) AF: 0.812 AC: 1715 AN: 2112

Alfa AF: 0.849 Hom.: 90696

Bravo AF: 0.784

Asia WGS AF: 0.665 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1858309; hg19: chr5-90556558;