5-91261216-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 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.464-16206C>G		intron	N/A
	LUCAT1	ENST00000648385.1		n.367+52422C>G		intron	N/A
	LUCAT1	ENST00000648822.1		n.487+3447C>G		intron	N/A

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

African (AFR) AF: 0.708 AC: 28496 AN: 40272

American (AMR) AF: 0.749 AC: 10913 AN: 14564

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3149 AN: 3464

East Asian (EAS) AF: 0.572 AC: 2774 AN: 4850

South Asian (SAS) AF: 0.764 AC: 3586 AN: 4692

European-Finnish (FIN) AF: 0.889 AC: 8619 AN: 9698

Middle Eastern (MID) AF: 0.830 AC: 239 AN: 288

European-Non Finnish (NFE) AF: 0.875 AC: 59299 AN: 67800

Other (OTH) AF: 0.814 AC: 1690 AN: 2076

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.57
PhyloP100		-0.51

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: rs7709572;

hg19: chr5-90557033;