chr22-41254367-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002883.4(RANGAP1):āc.1201C>Gā(p.Arg401Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00281 in 1,613,920 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_002883.4 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 |
---|---|---|---|---|---|---|---|
RANGAP1 | NM_002883.4 | c.1201C>G | p.Arg401Gly | missense_variant | 11/16 | ENST00000356244.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANGAP1 | ENST00000356244.8 | c.1201C>G | p.Arg401Gly | missense_variant | 11/16 | 1 | NM_002883.4 | P1 | |
RANGAP1 | ENST00000405486.5 | c.1201C>G | p.Arg401Gly | missense_variant | 12/17 | 1 | P1 | ||
RANGAP1 | ENST00000455915.6 | c.1201C>G | p.Arg401Gly | missense_variant | 10/15 | 1 | P1 | ||
RANGAP1 | ENST00000705116.1 | c.1201C>G | p.Arg401Gly | missense_variant | 11/16 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0143 AC: 2177AN: 151962Hom.: 49 Cov.: 31
GnomAD3 exomes AF: 0.00395 AC: 983AN: 248950Hom.: 23 AF XY: 0.00281 AC XY: 379AN XY: 134782
GnomAD4 exome AF: 0.00161 AC: 2357AN: 1461840Hom.: 60 Cov.: 33 AF XY: 0.00142 AC XY: 1031AN XY: 727220
GnomAD4 genome AF: 0.0143 AC: 2179AN: 152080Hom.: 49 Cov.: 31 AF XY: 0.0136 AC XY: 1008AN XY: 74330
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at