chr2-151610873-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001164507.2(NEB):c.11806-7C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,560,898 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_001164507.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.11806-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000427231.7 | NP_001157979.2 | |||
NEB | NM_001164508.2 | c.11806-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000397345.8 | NP_001157980.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.11806-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001164508.2 | ENSP00000380505 | P5 | |||
NEB | ENST00000427231.7 | c.11806-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001164507.2 | ENSP00000416578 | A2 | |||
NEB | ENST00000409198.5 | c.11077-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000386259 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000211 AC: 4AN: 189850Hom.: 0 AF XY: 0.0000198 AC XY: 2AN XY: 100968
GnomAD4 exome AF: 0.0000248 AC: 35AN: 1408778Hom.: 0 Cov.: 29 AF XY: 0.0000287 AC XY: 20AN XY: 696490
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 24, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at