rs10514346

Variant names:

• chr5-91192850-A-G
• rs10514346
• ENST00000647807.1:n.962+9761T>C

Variant summary

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

The ENST00000647807.1(LUCAT1):​n.962+9761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,280 control chromosomes in the GnomAD database, including 482 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 0.074 (482 hom., cov: 32)
• Consequence: LUCAT1 ENST00000647807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUCAT1	ENST00000647807.1		n.962+9761T>C		intron	N/A
	LUCAT1	ENST00000648385.1		n.710+2646T>C		intron	N/A
	LUCAT1	ENST00000649322.1		n.567-40662T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11288 AN: 152162 Hom.: 479 Cov.: 32

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0519

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0743 AC: 11320 AN: 152280 Hom.: 482 Cov.: 32 AF XY: 0.0738 AC XY: 5499 AN XY: 74466

African (AFR) AF: 0.0622 AC: 2585 AN: 41580

American (AMR) AF: 0.0910 AC: 1391 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.176 AC: 912 AN: 5176

South Asian (SAS) AF: 0.0522 AC: 252 AN: 4828

European-Finnish (FIN) AF: 0.0480 AC: 510 AN: 10618

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0721 AC: 4902 AN: 68000

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0735 Hom.: 820

Bravo AF: 0.0774

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.39
PhyloP100		-0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10514346;

hg19: chr5-90488667;