chr1-43352210-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_005373.3(MPL):c.1566-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,611,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005373.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPL | ENST00000372470.9 | c.1566-6C>T | splice_region_variant, intron_variant | Intron 10 of 11 | 1 | NM_005373.3 | ENSP00000361548.3 | |||
MPL | ENST00000413998.7 | c.1545-6C>T | splice_region_variant, intron_variant | Intron 10 of 11 | 1 | ENSP00000414004.3 | ||||
MPL | ENST00000643351.1 | c.222-6C>T | splice_region_variant, intron_variant | Intron 2 of 3 | ENSP00000495154.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459740Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726240
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
Essential thrombocythemia;C1327915:Congenital amegakaryocytic thrombocytopenia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at