1-204944332-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_001005388.3(NFASC):c.17C>T(p.Pro6Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P6P) has been classified as Likely benign.
Frequency
Consequence
NM_001005388.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFASC | NM_001005388.3 | c.17C>T | p.Pro6Leu | missense_variant | 3/30 | ENST00000339876.11 | NP_001005388.2 | |
NFASC | NM_001160331.2 | c.17C>T | p.Pro6Leu | missense_variant | 2/28 | ENST00000539706.6 | NP_001153803.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFASC | ENST00000339876.11 | c.17C>T | p.Pro6Leu | missense_variant | 3/30 | 5 | NM_001005388.3 | ENSP00000344786.6 | ||
NFASC | ENST00000539706.6 | c.17C>T | p.Pro6Leu | missense_variant | 2/28 | 5 | NM_001160331.2 | ENSP00000438614.2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249214Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134900
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461356Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 726926
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74480
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 30, 2024 | The c.17C>T (p.P6L) alteration is located in exon 3 (coding exon 1) of the NFASC gene. This alteration results from a C to T substitution at nucleotide position 17, causing the proline (P) at amino acid position 6 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at