chr1-174305008-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366446.1(RABGAP1L):c.1346A>T(p.Asn449Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,557,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366446.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RABGAP1L | NM_001366446.1 | c.1346A>T | p.Asn449Ile | missense_variant | 11/26 | ENST00000681986.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RABGAP1L | ENST00000681986.1 | c.1346A>T | p.Asn449Ile | missense_variant | 11/26 | NM_001366446.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000197 AC: 4AN: 203078Hom.: 0 AF XY: 0.0000270 AC XY: 3AN XY: 111032
GnomAD4 exome AF: 0.00000498 AC: 7AN: 1405362Hom.: 0 Cov.: 30 AF XY: 0.00000573 AC XY: 4AN XY: 697622
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 15, 2024 | The c.1346A>T (p.N449I) alteration is located in exon 1 (coding exon 1) of the RABGAP1L gene. This alteration results from a A to T substitution at nucleotide position 1346, causing the asparagine (N) at amino acid position 449 to be replaced by an isoleucine (I). 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