chr10-113634189-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_198060.4(NRAP):c.1450G>A(p.Asp484Asn) variant causes a missense change. The variant allele was found at a frequency of 0.134 in 1,611,454 control chromosomes in the GnomAD database, including 16,538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_198060.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRAP | NM_198060.4 | c.1450G>A | p.Asp484Asn | missense_variant | 15/42 | ENST00000359988.4 | NP_932326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRAP | ENST00000359988.4 | c.1450G>A | p.Asp484Asn | missense_variant | 15/42 | 1 | NM_198060.4 | ENSP00000353078.3 | ||
NRAP | ENST00000369358.8 | c.1450G>A | p.Asp484Asn | missense_variant | 15/42 | 1 | ENSP00000358365.4 | |||
NRAP | ENST00000360478.7 | c.1345G>A | p.Asp449Asn | missense_variant | 14/41 | 1 | ENSP00000353666.3 | |||
NRAP | ENST00000369360.7 | c.1345G>A | p.Asp449Asn | missense_variant | 14/41 | 5 | ENSP00000358367.3 |
Frequencies
GnomAD3 genomes AF: 0.179 AC: 27231AN: 151946Hom.: 2963 Cov.: 32
GnomAD3 exomes AF: 0.150 AC: 37786AN: 251254Hom.: 3268 AF XY: 0.151 AC XY: 20460AN XY: 135796
GnomAD4 exome AF: 0.130 AC: 189434AN: 1459390Hom.: 13573 Cov.: 30 AF XY: 0.131 AC XY: 95334AN XY: 726142
GnomAD4 genome AF: 0.179 AC: 27249AN: 152064Hom.: 2965 Cov.: 32 AF XY: 0.178 AC XY: 13211AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
NRAP-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at