17-49510444-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002507.4(NGFR):c.601C>G(p.Pro201Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,613,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002507.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NGFR | NM_002507.4 | c.601C>G | p.Pro201Ala | missense_variant | 4/6 | ENST00000172229.8 | |
NGFR-AS1 | NR_103773.1 | n.377+539G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NGFR | ENST00000172229.8 | c.601C>G | p.Pro201Ala | missense_variant | 4/6 | 1 | NM_002507.4 | P1 | |
NGFR-AS1 | ENST00000514506.1 | n.377+539G>C | intron_variant, non_coding_transcript_variant | 2 | |||||
NGFR | ENST00000504201.1 | c.319C>G | p.Pro107Ala | missense_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250978Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135706
GnomAD4 exome AF: 0.000101 AC: 148AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.0000949 AC XY: 69AN XY: 727184
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.601C>G (p.P201A) alteration is located in exon 4 (coding exon 4) of the NGFR gene. This alteration results from a C to G substitution at nucleotide position 601, causing the proline (P) at amino acid position 201 to be replaced by an alanine (A). 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