1-108470617-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143988.2(NBPF6):c.1896G>T(p.Arg632Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000836 in 1,554,950 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001143988.2 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 | UniProt |
---|---|---|---|---|---|---|---|
NBPF6 | NM_001143988.2 | c.1896G>T | p.Arg632Ser | missense_variant | 15/15 | ENST00000495380.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBPF6 | ENST00000495380.7 | c.1896G>T | p.Arg632Ser | missense_variant | 15/15 | 5 | NM_001143988.2 | ||
NBPF6 | ENST00000370040.7 | c.1983G>T | p.Arg661Ser | missense_variant | 16/16 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000179 AC: 3AN: 167592Hom.: 0 AF XY: 0.0000113 AC XY: 1AN XY: 88466
GnomAD4 exome AF: 0.00000784 AC: 11AN: 1402840Hom.: 0 Cov.: 30 AF XY: 0.0000101 AC XY: 7AN XY: 692352
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 26 AF XY: 0.0000269 AC XY: 2AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2023 | The c.1983G>T (p.R661S) alteration is located in exon 16 (coding exon 15) of the NBPF6 gene. This alteration results from a G to T substitution at nucleotide position 1983, causing the arginine (R) at amino acid position 661 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