rs10514346

chr5-91192850-A-G

Variant summary

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

The ENST00000650150.1(LUCAT1):n.380-40662T>C variant causes a intron, non coding transcript 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 ENST00000650150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

Genes affected

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

LOC107986432 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986432	XR_001742795.2	n.1207+2646T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LUCAT1	ENST00000650150.1	n.380-40662T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0622

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0522

Gnomad4 FIN AF: 0.0480

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0726 Hom.: 555

Bravo AF: 0.0774

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.46
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514346; hg19: chr5-90488667;