chr1-3463265-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014448.4(ARHGEF16):c.181C>T(p.Arg61Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,549,636 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014448.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF16 | NM_014448.4 | c.181C>T | p.Arg61Trp | missense_variant | Exon 2 of 15 | ENST00000378378.9 | NP_055263.2 | |
ARHGEF16 | XM_017001049.2 | c.232C>T | p.Arg78Trp | missense_variant | Exon 2 of 15 | XP_016856538.1 | ||
ARHGEF16 | XM_017001051.2 | c.181C>T | p.Arg61Trp | missense_variant | Exon 2 of 15 | XP_016856540.1 | ||
ARHGEF16 | XM_047418009.1 | c.232C>T | p.Arg78Trp | missense_variant | Exon 2 of 8 | XP_047273965.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000464 AC: 7AN: 150798Hom.: 0 AF XY: 0.0000622 AC XY: 5AN XY: 80396
GnomAD4 exome AF: 0.0000200 AC: 28AN: 1397330Hom.: 1 Cov.: 31 AF XY: 0.0000247 AC XY: 17AN XY: 689164
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.181C>T (p.R61W) alteration is located in exon 2 (coding exon 1) of the ARHGEF16 gene. This alteration results from a C to T substitution at nucleotide position 181, causing the arginine (R) at amino acid position 61 to be replaced by a tryptophan (W). 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