ENST00000647807.1:n.962+9761T>C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986432	XR_001742795.2	n.1207+2646T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUCAT1	ENST00000647807.1	n.962+9761T>C		intron_variant	Intron 6 of 6
LUCAT1	ENST00000648385.1	n.710+2646T>C		intron_variant	Intron 5 of 5
LUCAT1	ENST00000649322.1	n.567-40662T>C		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs10514346; hg19: chr5-90488667;