rs13144621

Variant names:

• chr4-108296773-T-C
• rs13144621
• ENST00000732953.1:n.594-7868T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-108296773-T-C
• chr4-108296773-T-G

Variant summary

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

The ENST00000732953.1(LEF1-AS1):​n.594-7868T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,988 control chromosomes in the GnomAD database, including 30,928 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 0.63 (30928 hom., cov: 31)
• Consequence: LEF1-AS1 ENST00000732953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LEF1-AS1	ENST00000732953.1	n.594-7868T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95077 AN: 151870 Hom.: 30910 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.626 AC: 95124 AN: 151988 Hom.: 30928 Cov.: 31 AF XY: 0.629 AC XY: 46750 AN XY: 74278

African (AFR) AF: 0.443 AC: 18352 AN: 41434

American (AMR) AF: 0.728 AC: 11124 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2559 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4278 AN: 5174

South Asian (SAS) AF: 0.690 AC: 3316 AN: 4806

European-Finnish (FIN) AF: 0.705 AC: 7443 AN: 10564

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45848 AN: 67956

Other (OTH) AF: 0.658 AC: 1385 AN: 2106

Alfa AF: 0.620 Hom.: 8784

Bravo AF: 0.626

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.22
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs13144621; hg19: chr4-109217929;