10-68199581-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032578.4(MYPN):c.3493+6G>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 0.000012 in 1,582,742 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 (no stars).
Frequency
Consequence
NM_032578.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYPN | NM_032578.4 | c.3493+6G>T | splice_region_variant, intron_variant | Intron 17 of 19 | ENST00000358913.10 | NP_115967.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000246 AC: 3AN: 121732Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000198 AC: 4AN: 201692Hom.: 0 AF XY: 0.0000369 AC XY: 4AN XY: 108544
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1461010Hom.: 0 Cov.: 40 AF XY: 0.0000110 AC XY: 8AN XY: 726846
GnomAD4 genome AF: 0.0000246 AC: 3AN: 121732Hom.: 0 Cov.: 30 AF XY: 0.0000507 AC XY: 3AN XY: 59202
ClinVar
Submissions by phenotype
not specified Benign:1
- -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at