rs9997081

chr4-108205397-T-Achr4-108205397-T-Cchr4-108205397-T-G

Variant summary

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

The ENST00000665040.2(LEF1-AS1):n.328+5438T>A variant causes a intron, non coding transcript 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 ENST00000665040.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LEF1-AS1	ENST00000665040.2	n.328+5438T>A		intron_variant, non_coding_transcript_variant
LEF1-AS1	ENST00000512129.2	n.238+5438T>A		intron_variant, non_coding_transcript_variant		3
LEF1-AS1	ENST00000693123.1	n.451+5438T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.852

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.5
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9997081; hg19: chr4-109126553;