5-149616754-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001001669.3(ARHGEF37):c.646C>T(p.Arg216Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000824 in 1,601,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R216H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001001669.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF37 | NM_001001669.3 | c.646C>T | p.Arg216Cys | missense_variant | 5/13 | ENST00000333677.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF37 | ENST00000333677.7 | c.646C>T | p.Arg216Cys | missense_variant | 5/13 | 2 | NM_001001669.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 30AN: 247696Hom.: 0 AF XY: 0.0000967 AC XY: 13AN XY: 134376
GnomAD4 exome AF: 0.0000711 AC: 103AN: 1448986Hom.: 0 Cov.: 31 AF XY: 0.0000682 AC XY: 49AN XY: 718332
GnomAD4 genome AF: 0.000191 AC: 29AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.646C>T (p.R216C) alteration is located in exon 5 (coding exon 4) of the ARHGEF37 gene. This alteration results from a C to T substitution at nucleotide position 646, causing the arginine (R) at amino acid position 216 to be replaced by a cysteine (C). 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