X-19360739-C-CTGAT
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001001671.4(MAP3K15):c.*6_*9dupATCA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000604 in 1,192,552 control chromosomes in the GnomAD database, including 1 homozygotes. There are 21 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001001671.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP3K15 | NM_001001671.4 | c.*6_*9dupATCA | 3_prime_UTR_variant | Exon 29 of 29 | ENST00000338883.9 | NP_001001671.3 | ||
PDHA1 | NM_000284.4 | c.*1089_*1092dupATTG | 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.*6_*9dupATCA | 3_prime_UTR_variant | Exon 29 of 29 | 5 | NM_001001671.4 | ENSP00000345629.4 | |||
PDHA1 | ENST00000422285.7 | c.*1089_*1092dupATTG | 3_prime_UTR_variant | Exon 11 of 11 | 1 | NM_000284.4 | ENSP00000394382.2 |
Frequencies
GnomAD3 genomes AF: 0.0000714 AC: 8AN: 112055Hom.: 0 Cov.: 24 AF XY: 0.0000584 AC XY: 2AN XY: 34233
GnomAD3 exomes AF: 0.0000567 AC: 10AN: 176414Hom.: 0 AF XY: 0.0000321 AC XY: 2AN XY: 62394
GnomAD4 exome AF: 0.0000592 AC: 64AN: 1080443Hom.: 1 Cov.: 25 AF XY: 0.0000546 AC XY: 19AN XY: 347789
GnomAD4 genome AF: 0.0000714 AC: 8AN: 112109Hom.: 0 Cov.: 24 AF XY: 0.0000583 AC XY: 2AN XY: 34297
ClinVar
Submissions by phenotype
PDHA1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at