10-113589078-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198060.4(NRAP):c.5090G>C(p.Arg1697Pro) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198060.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRAP | NM_198060.4 | c.5090G>C | p.Arg1697Pro | missense_variant, splice_region_variant | Exon 42 of 42 | ENST00000359988.4 | NP_932326.2 | |
HABP2 | NM_004132.5 | c.*709C>G | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000351270.4 | NP_004123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRAP | ENST00000359988.4 | c.5090G>C | p.Arg1697Pro | missense_variant, splice_region_variant | Exon 42 of 42 | 1 | NM_198060.4 | ENSP00000353078.3 | ||
HABP2 | ENST00000351270.4 | c.*709C>G | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_004132.5 | ENSP00000277903.4 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250560Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135424
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461274Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 726988
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74304
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.5090G>C (p.R1697P) alteration is located in exon 42 (coding exon 42) of the NRAP gene. This alteration results from a G to C substitution at nucleotide position 5090, causing the arginine (R) at amino acid position 1697 to be replaced by a proline (P). 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