4-40102923-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018177.6(N4BP2):c.1078C>T(p.Pro360Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,890 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_018177.6 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 |
---|---|---|---|---|---|---|---|
N4BP2 | NM_018177.6 | c.1078C>T | p.Pro360Ser | missense_variant | 4/18 | ENST00000261435.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
N4BP2 | ENST00000261435.11 | c.1078C>T | p.Pro360Ser | missense_variant | 4/18 | 5 | NM_018177.6 | P1 | |
N4BP2 | ENST00000513269.1 | c.19C>T | p.Pro7Ser | missense_variant | 1/15 | 1 | |||
N4BP2 | ENST00000511480.5 | c.*869C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/19 | 1 | ||||
N4BP2 | ENST00000706658.1 | c.*869C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/21 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251482Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135914
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461890Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1078C>T (p.P360S) alteration is located in exon 4 (coding exon 2) of the N4BP2 gene. This alteration results from a C to T substitution at nucleotide position 1078, causing the proline (P) at amino acid position 360 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