1-16592006-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001405667.2(NBPF1):c.16G>A(p.Gly6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000665 in 150,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001405667.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NBPF1 | NM_001405667.2 | c.16G>A | p.Gly6Ser | missense_variant | 7/29 | NP_001392596.1 | ||
NBPF1 | NM_001405680.2 | c.16G>A | p.Gly6Ser | missense_variant | 7/29 | NP_001392609.1 | ||
NBPF1 | NM_001405681.2 | c.16G>A | p.Gly6Ser | missense_variant | 7/29 | NP_001392610.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NBPF1 | ENST00000430580.6 | c.16G>A | p.Gly6Ser | missense_variant | 7/29 | 5 | ENSP00000474456.1 | |||
NBPF1 | ENST00000392963.5 | n.16G>A | non_coding_transcript_exon_variant | 4/19 | 5 | ENSP00000473795.1 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150382Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249688Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135400
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.85e-7 AC: 1AN: 1459540Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 726156
GnomAD4 genome AF: 0.00000665 AC: 1AN: 150382Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 24, 2024 | The c.16G>A (p.G6S) alteration is located in exon 7 (coding exon 1) of the NBPF1 gene. This alteration results from a G to A substitution at nucleotide position 16, causing the glycine (G) at amino acid position 6 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