chr1-155212373-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002455.5(MTX1):c.772-12C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 1,613,036 control chromosomes in the GnomAD database, including 229,926 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002455.5 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTX1 | NM_002455.5 | c.772-12C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000368376.8 | |||
MTX1 | NM_198883.3 | c.679-12C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTX1 | ENST00000368376.8 | c.772-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002455.5 | ||||
ENST00000455788.1 | n.181-835G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.568 AC: 86296AN: 151944Hom.: 24877 Cov.: 32
GnomAD3 exomes AF: 0.565 AC: 141978AN: 251214Hom.: 41347 AF XY: 0.553 AC XY: 75146AN XY: 135782
GnomAD4 exome AF: 0.525 AC: 767367AN: 1460974Hom.: 205010 Cov.: 66 AF XY: 0.523 AC XY: 380045AN XY: 726650
GnomAD4 genome AF: 0.568 AC: 86381AN: 152062Hom.: 24916 Cov.: 32 AF XY: 0.570 AC XY: 42342AN XY: 74320
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at