5-91261216-G-C

Variant names:

• chr5-91261216-G-C
• rs7709572
• ENST00000647807.1:n.464-16206C>G

Variant summary

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

The ENST00000647807.1(LUCAT1):​n.464-16206C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 148,610 control chromosomes in the GnomAD database, including 48,549 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 (48549 hom., cov: 25)
• Consequence: LUCAT1 ENST00000647807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986432	XR_001742795.2	n.611+3447C>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUCAT1	ENST00000647807.1	n.464-16206C>G		intron_variant	Intron 2 of 6
LUCAT1	ENST00000648385.1	n.367+52422C>G		intron_variant	Intron 2 of 5
LUCAT1	ENST00000648822.1	n.487+3447C>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.805 AC: 119512 AN: 148506 Hom.: 48521 Cov.: 25

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.805 AC: 119588 AN: 148610 Hom.: 48549 Cov.: 25 AF XY: 0.803 AC XY: 57963 AN XY: 72196

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.814

Alfa AF: 0.816 Hom.: 2570

Bravo AF: 0.784

Asia WGS AF: 0.664 AC: 2310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7709572; hg19: chr5-90557033;