chr3-51385380-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006010.6(MANF):c.38C>T(p.Ala13Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,238,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006010.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MANF | ENST00000528157.7 | c.38C>T | p.Ala13Val | missense_variant | Exon 1 of 4 | 1 | NM_006010.6 | ENSP00000432799.3 | ||
MANF | ENST00000446668.5 | n.23C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 | ENSP00000405280.1 | ||||
MANF | ENST00000470900.1 | n.-29C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151550Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000166 AC: 18AN: 1087308Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 7AN XY: 514502
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151656Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74144
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.38C>T (p.A13V) alteration is located in exon 1 (coding exon 1) of the MANF gene. This alteration results from a C to T substitution at nucleotide position 38, causing the alanine (A) at amino acid position 13 to be replaced by a valine (V). 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