rs9997081

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-108205397-T-A
• chr4-108205397-T-C
• chr4-108205397-T-G

Variant summary

Our verdict is Benign. Variant got -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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LEF1-AS1	ENST00000512129.2	n.238+5438T>A		intron_variant	Intron 2 of 2	3
LEF1-AS1	ENST00000665040.2	n.328+5438T>A		intron_variant	Intron 3 of 3
LEF1-AS1	ENST00000693123.1	n.451+5438T>A		intron_variant	Intron 4 of 4

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;