X-19360178-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001001671.4(MAP3K15):c.*571G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00381 in 148,505 control chromosomes in the GnomAD database, including 1 homozygotes. There are 153 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001001671.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP3K15 | NM_001001671.4 | c.*571G>C | 3_prime_UTR_variant | Exon 29 of 29 | ENST00000338883.9 | NP_001001671.3 | ||
PDHA1 | NM_000284.4 | c.*525C>G | 3_prime_UTR_variant | Exon 11 of 11 | ENST00000422285.7 | NP_000275.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP3K15 | ENST00000338883 | c.*571G>C | 3_prime_UTR_variant | Exon 29 of 29 | 5 | NM_001001671.4 | ENSP00000345629.4 | |||
PDHA1 | ENST00000422285.7 | c.*525C>G | 3_prime_UTR_variant | Exon 11 of 11 | 1 | NM_000284.4 | ENSP00000394382.2 |
Frequencies
GnomAD3 genomes AF: 0.00373 AC: 421AN: 112755Hom.: 1 Cov.: 24 AF XY: 0.00370 AC XY: 129AN XY: 34895
GnomAD4 exome AF: 0.00406 AC: 145AN: 35697Hom.: 0 Cov.: 0 AF XY: 0.00352 AC XY: 24AN XY: 6821
GnomAD4 genome AF: 0.00373 AC: 421AN: 112808Hom.: 1 Cov.: 24 AF XY: 0.00369 AC XY: 129AN XY: 34958
ClinVar
Submissions by phenotype
Pyruvate dehydrogenase E1-alpha deficiency Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at