2-110115780-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005434.5(MALL):c.13G>T(p.Asp5Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000894 in 1,118,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005434.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MALL | NM_005434.5 | c.13G>T | p.Asp5Tyr | missense_variant | Exon 1 of 4 | ENST00000272462.3 | NP_005425.1 | |
MALL | NM_001371560.1 | c.13G>T | p.Asp5Tyr | missense_variant | Exon 1 of 3 | NP_001358489.1 | ||
MALL | NM_001371559.1 | c.93+2237G>T | intron_variant | Intron 1 of 3 | NP_001358488.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MALL | ENST00000272462.3 | c.13G>T | p.Asp5Tyr | missense_variant | Exon 1 of 4 | 1 | NM_005434.5 | ENSP00000272462.2 | ||
MALL | ENST00000427178.1 | c.13G>T | p.Asp5Tyr | missense_variant | Exon 1 of 2 | 1 | ENSP00000400518.1 | |||
MALL | ENST00000424988.1 | n.13G>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 | ENSP00000394792.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151470Hom.: 0 Cov.: 30 FAILED QC
GnomAD4 exome AF: 8.94e-7 AC: 1AN: 1118342Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 531012
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151582Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74032
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.13G>T (p.D5Y) alteration is located in exon 1 (coding exon 1) of the MALL gene. This alteration results from a G to T substitution at nucleotide position 13, causing the aspartic acid (D) at amino acid position 5 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.