rs7683465

Variant names:

• chr4-108302381-G-A
• rs7683465
• ENST00000732953.1:n.594-2260G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-108302381-G-A
• chr4-108302381-G-C
• chr4-108302381-G-T

Variant summary

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

The ENST00000732953.1(LEF1-AS1):​n.594-2260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,062 control chromosomes in the GnomAD database, including 28,457 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 0.58 (28457 hom., cov: 32)
• Consequence: LEF1-AS1 ENST00000732953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732953.1. 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
	LEF1-AS1	ENST00000732953.1		n.594-2260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88627 AN: 151944 Hom.: 28441 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.583 AC: 88655 AN: 152062 Hom.: 28457 Cov.: 32 AF XY: 0.589 AC XY: 43739 AN XY: 74312

African (AFR) AF: 0.298 AC: 12340 AN: 41450

American (AMR) AF: 0.710 AC: 10848 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4277 AN: 5170

South Asian (SAS) AF: 0.686 AC: 3310 AN: 4822

European-Finnish (FIN) AF: 0.705 AC: 7458 AN: 10584

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.673 AC: 45741 AN: 67980

Other (OTH) AF: 0.625 AC: 1318 AN: 2108

Alfa AF: 0.591 Hom.: 4272

Bravo AF: 0.576

Asia WGS AF: 0.758 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.67

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: rs7683465;

hg19: chr4-109223537;

COSMIC: COSV107199874;