chr12-53506856-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003717.4(NPFF):āc.262T>Cā(p.Trp88Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,604,760 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003717.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFF | NM_003717.4 | c.262T>C | p.Trp88Arg | missense_variant | 3/3 | ENST00000267017.4 | |
ATF7-NPFF | NR_159377.1 | n.2053T>C | non_coding_transcript_exon_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFF | ENST00000267017.4 | c.262T>C | p.Trp88Arg | missense_variant | 3/3 | 1 | NM_003717.4 | P1 | |
NPFF | ENST00000448979.4 | n.502T>C | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0191 AC: 2901AN: 152140Hom.: 71 Cov.: 32
GnomAD3 exomes AF: 0.00728 AC: 1769AN: 242936Hom.: 37 AF XY: 0.00584 AC XY: 765AN XY: 131086
GnomAD4 exome AF: 0.00291 AC: 4229AN: 1452502Hom.: 86 Cov.: 31 AF XY: 0.00266 AC XY: 1918AN XY: 721782
GnomAD4 genome AF: 0.0191 AC: 2904AN: 152258Hom.: 71 Cov.: 32 AF XY: 0.0177 AC XY: 1321AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at