rs17414315
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_006267.5(RANBP2):āc.2173A>Gā(p.Ser725Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,611,980 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S725T) has been classified as Uncertain significance.
Frequency
Consequence
NM_006267.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP2 | NM_006267.5 | c.2173A>G | p.Ser725Gly | missense_variant | 15/29 | ENST00000283195.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.2173A>G | p.Ser725Gly | missense_variant | 15/29 | 1 | NM_006267.5 | P1 | |
RANBP2 | ENST00000697737.1 | c.2173A>G | p.Ser725Gly | missense_variant | 15/27 | ||||
RANBP2 | ENST00000697740.1 | c.2095A>G | p.Ser699Gly | missense_variant | 15/27 |
Frequencies
GnomAD3 genomes ? AF: 0.00867 AC: 1319AN: 152218Hom.: 23 Cov.: 31
GnomAD3 exomes AF: 0.00218 AC: 543AN: 249538Hom.: 5 AF XY: 0.00160 AC XY: 217AN XY: 135440
GnomAD4 exome AF: 0.000854 AC: 1247AN: 1459644Hom.: 9 Cov.: 34 AF XY: 0.000756 AC XY: 549AN XY: 726124
GnomAD4 genome ? AF: 0.00874 AC: 1331AN: 152336Hom.: 23 Cov.: 31 AF XY: 0.00846 AC XY: 630AN XY: 74490
ClinVar
Submissions by phenotype
Familial acute necrotizing encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at