3-52478251-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_007184.4(NISCH):c.1142A>G(p.Asn381Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NISCH | NM_007184.4 | c.1142A>G | p.Asn381Ser | missense_variant | 10/21 | ENST00000345716.9 | |
NISCH | NM_001276293.2 | c.1142A>G | p.Asn381Ser | missense_variant | 10/13 | ||
NISCH | NM_001276294.2 | c.1142A>G | p.Asn381Ser | missense_variant | 10/14 | ||
NISCH | XM_047447373.1 | c.1142A>G | p.Asn381Ser | missense_variant | 10/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NISCH | ENST00000345716.9 | c.1142A>G | p.Asn381Ser | missense_variant | 10/21 | 1 | NM_007184.4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251290Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135800
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727214
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.1142A>G (p.N381S) alteration is located in exon 10 (coding exon 10) of the NISCH gene. This alteration results from a A to G substitution at nucleotide position 1142, causing the asparagine (N) at amino acid position 381 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