NM_013335.4:c.40+15G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013335.4(GMPPA):c.40+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,613,362 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_013335.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GMPPA | NM_013335.4 | c.40+15G>A | intron_variant | Intron 2 of 12 | ENST00000313597.10 | NP_037467.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00908 AC: 1382AN: 152120Hom.: 21 Cov.: 32
GnomAD3 exomes AF: 0.00246 AC: 619AN: 251420Hom.: 10 AF XY: 0.00182 AC XY: 247AN XY: 135902
GnomAD4 exome AF: 0.00101 AC: 1479AN: 1461124Hom.: 26 Cov.: 30 AF XY: 0.000876 AC XY: 637AN XY: 726906
GnomAD4 genome AF: 0.00908 AC: 1383AN: 152238Hom.: 21 Cov.: 32 AF XY: 0.00857 AC XY: 638AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Alacrima, achalasia, and intellectual disability syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at