17-46751533-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_006178.4(NSF):c.2074A>G(p.Thr692Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006178.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSF | NM_006178.4 | c.2074A>G | p.Thr692Ala | missense_variant | 19/21 | ENST00000398238.8 | |
LRRC37A2 | XM_024450773.2 | c.4809+201014A>G | intron_variant | ||||
NSF | NR_040116.2 | n.2141A>G | non_coding_transcript_exon_variant | 18/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSF | ENST00000398238.8 | c.2074A>G | p.Thr692Ala | missense_variant | 19/21 | 1 | NM_006178.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249376Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135288
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461772Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727172
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.2074A>G (p.T692A) alteration is located in exon 19 (coding exon 19) of the NSF gene. This alteration results from a A to G substitution at nucleotide position 2074, causing the threonine (T) at amino acid position 692 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