19-49061841-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006179.5(NTF4):c.157C>T(p.Pro53Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,398,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006179.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTF4 | NM_006179.5 | c.157C>T | p.Pro53Ser | missense_variant | Exon 2 of 2 | ENST00000593537.2 | NP_006170.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTF4 | ENST00000593537.2 | c.157C>T | p.Pro53Ser | missense_variant | Exon 2 of 2 | 6 | NM_006179.5 | ENSP00000469455.1 | ||
ENSG00000283663 | ENST00000599795.5 | n.157C>T | non_coding_transcript_exon_variant | Exon 3 of 7 | 2 | ENSP00000470689.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000134 AC: 2AN: 148966Hom.: 0 AF XY: 0.0000251 AC XY: 2AN XY: 79774
GnomAD4 exome AF: 0.0000157 AC: 22AN: 1398420Hom.: 0 Cov.: 32 AF XY: 0.0000188 AC XY: 13AN XY: 689878
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.157C>T (p.P53S) alteration is located in exon 2 (coding exon 1) of the NTF4 gene. This alteration results from a C to T substitution at nucleotide position 157, causing the proline (P) at amino acid position 53 to be replaced by a serine (S). 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