chr5-91262549-A-T

Variant names:

• chr5-91262549-A-T
• rs7724489
• ENST00000647807.1:n.464-17539T>A

Variant summary

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

The ENST00000647807.1(LUCAT1):​n.464-17539T>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 151,906 control chromosomes in the GnomAD database, including 49,373 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 (49373 hom., cov: 29)
• Consequence: LUCAT1 ENST00000647807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 2 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=-1.05).
• 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.464-17539T>A		intron	N/A
	LUCAT1	ENST00000648385.1		n.367+51089T>A		intron	N/A
	LUCAT1	ENST00000648822.1		n.487+2114T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121463 AN: 151786 Hom.: 49343 Cov.: 29

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.888

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: 121544 AN: 151906 Hom.: 49373 Cov.: 29 AF XY: 0.799 AC XY: 59286 AN XY: 74210

African (AFR) AF: 0.702 AC: 29052 AN: 41384

American (AMR) AF: 0.747 AC: 11398 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3149 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2741 AN: 5112

South Asian (SAS) AF: 0.751 AC: 3621 AN: 4822

European-Finnish (FIN) AF: 0.888 AC: 9386 AN: 10570

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

European-Non Finnish (NFE) AF: 0.874 AC: 59417 AN: 67972

Other (OTH) AF: 0.811 AC: 1715 AN: 2114

Alfa AF: 0.820 Hom.: 2717

Bravo AF: 0.784

Asia WGS AF: 0.658 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.35
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7724489; hg19: chr5-90558366;