rs199455
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_006178.4(NSF):c.1762-4699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,542 control chromosomes in the GnomAD database, including 32,771 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.63 ( 32771 hom., cov: 29)
Exomes 𝑓: 0.73 ( 393452 hom. )
Failed GnomAD Quality Control
Consequence
NSF
NM_006178.4 intron
NM_006178.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.50
Genes affected
NSF (HGNC:8016): (N-ethylmaleimide sensitive factor, vesicle fusing ATPase) Enables PDZ domain binding activity and ionotropic glutamate receptor binding activity. Involved in intracellular protein transport; positive regulation of protein catabolic process; and positive regulation of receptor recycling. Located in Golgi apparatus; cytosol; and plasma membrane. Implicated in developmental and epileptic encephalopathy. [provided by Alliance of Genome Resources, Apr 2022]
RPS7P11 (HGNC:35841): (ribosomal protein S7 pseudogene 11)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSF | NM_006178.4 | c.1762-4699C>T | intron_variant | ENST00000398238.8 | |||
LRRC37A2 | XM_024450773.2 | c.4809+171331C>T | intron_variant | ||||
NSF | NR_040116.2 | n.1829-4699C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSF | ENST00000398238.8 | c.1762-4699C>T | intron_variant | 1 | NM_006178.4 | P3 | |||
RPS7P11 | ENST00000484240.1 | n.318G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.634 AC: 96041AN: 151422Hom.: 32766 Cov.: 29
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.735 AC: 1046757AN: 1424528Hom.: 393452 Cov.: 28 AF XY: 0.740 AC XY: 526426AN XY: 710970
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.634 AC: 96064AN: 151542Hom.: 32771 Cov.: 29 AF XY: 0.639 AC XY: 47297AN XY: 74002
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at