ENST00000512129.2:n.238+5438T>A

Variant names:

• chr4-108205397-T-A
• rs9997081
• ENST00000512129.2:n.238+5438T>A

Variant summary

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

The ENST00000512129.2(LEF1-AS1):​n.238+5438T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,138 control chromosomes in the GnomAD database, including 57,475 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 0.87 (57475 hom., cov: 31)
• Consequence: LEF1-AS1 ENST00000512129.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 3 publications found

Genes affected

LEF1-AS1 (HGNC:40339): (LEF1 antisense RNA 1)

ENSG00000295861 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512129.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEF1-AS1	ENST00000512129.2	TSL:3	n.238+5438T>A		intron	N/A
	LEF1-AS1	ENST00000665040.3		n.514+5438T>A		intron	N/A
	LEF1-AS1	ENST00000693123.2		n.552+5438T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131879 AN: 152018 Hom.: 57442 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.867 AC: 131968 AN: 152138 Hom.: 57475 Cov.: 31 AF XY: 0.868 AC XY: 64589 AN XY: 74382

African (AFR) AF: 0.770 AC: 31905 AN: 41454

American (AMR) AF: 0.904 AC: 13828 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3051 AN: 3468

East Asian (EAS) AF: 0.868 AC: 4490 AN: 5170

South Asian (SAS) AF: 0.876 AC: 4212 AN: 4810

European-Finnish (FIN) AF: 0.926 AC: 9822 AN: 10608

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61781 AN: 68024

Other (OTH) AF: 0.852 AC: 1798 AN: 2110

Alfa AF: 0.892 Hom.: 3006

Bravo AF: 0.861

Asia WGS AF: 0.851 AC: 2960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs9997081; hg19: chr4-109126553;