13-50713230-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198989.3(DLEU7):āc.470T>Cā(p.Leu157Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,458,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198989.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLEU7 | NM_198989.3 | c.470T>C | p.Leu157Pro | missense_variant | 2/2 | NP_945340.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLEU7 | ENST00000400393.3 | c.470T>C | p.Leu157Pro | missense_variant | 2/2 | 1 | ENSP00000420976.1 | |||
DLEU7 | ENST00000443723.1 | n.69T>C | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
DLEU1 | ENST00000650910.1 | n.1078A>G | non_coding_transcript_exon_variant | 2/4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242186Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131348
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1458844Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 725316
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.470T>C (p.L157P) alteration is located in exon 2 (coding exon 2) of the DLEU7 gene. This alteration results from a T to C substitution at nucleotide position 470, causing the leucine (L) at amino acid position 157 to be replaced by a proline (P). 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