chr17-31229025-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP2PP3
The NM_001042492.3(NF1):c.2410G>T(p.Ala804Ser) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000138 in 1,444,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A804P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001042492.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.2410G>T | p.Ala804Ser | missense_variant, splice_region_variant | 21/58 | ENST00000358273.9 | |
NF1 | NM_000267.3 | c.2410G>T | p.Ala804Ser | missense_variant, splice_region_variant | 21/57 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.2410G>T | p.Ala804Ser | missense_variant, splice_region_variant | 21/58 | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247128Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133768
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1444912Hom.: 0 Cov.: 31 AF XY: 0.00000279 AC XY: 2AN XY: 715586
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at