13-50843558-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001306135.2(DLEU7):c.89G>T(p.Trp30Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,482,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001306135.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLEU7 | NM_001306135.2 | c.89G>T | p.Trp30Leu | missense_variant | 1/2 | ENST00000504404.2 | NP_001293064.1 | |
DLEU7 | NM_198989.3 | c.89G>T | p.Trp30Leu | missense_variant | 1/2 | NP_945340.2 | ||
DLEU7-AS1 | NR_046551.1 | n.438+3464C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLEU7 | ENST00000504404.2 | c.89G>T | p.Trp30Leu | missense_variant | 1/2 | 1 | NM_001306135.2 | ENSP00000427177.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000252 AC: 2AN: 79318Hom.: 0 AF XY: 0.0000218 AC XY: 1AN XY: 45826
GnomAD4 exome AF: 0.0000504 AC: 67AN: 1330676Hom.: 0 Cov.: 32 AF XY: 0.0000472 AC XY: 31AN XY: 656196
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.89G>T (p.W30L) alteration is located in exon 1 (coding exon 1) of the DLEU7 gene. This alteration results from a G to T substitution at nucleotide position 89, causing the tryptophan (W) at amino acid position 30 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at