chr2-151674476-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_ModeratePM2PP3_Strong
The NM_001164507.2(NEB):c.3987+1G>T variant causes a splice donor change. The variant allele was found at a frequency of 0.000036 in 1,612,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001164507.2 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.3987+1G>T | splice_donor_variant | ENST00000427231.7 | |||
NEB | NM_001164508.2 | c.3987+1G>T | splice_donor_variant | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.3987+1G>T | splice_donor_variant | 5 | NM_001164508.2 | P5 | |||
NEB | ENST00000427231.7 | c.3987+1G>T | splice_donor_variant | 5 | NM_001164507.2 | A2 | |||
NEB | ENST00000409198.5 | c.3987+1G>T | splice_donor_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152248Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249226Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135202
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1460372Hom.: 0 Cov.: 29 AF XY: 0.0000358 AC XY: 26AN XY: 726592
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152248Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74380
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at