ENST00000378152.8:c.14C>A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000378152.8(ARHGEF1):c.14C>A(p.Ser5Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000618 in 1,607,670 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S5C) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000378152.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF1 | NM_004706.4 | c.-20+1192C>A | intron_variant | Intron 1 of 28 | ENST00000354532.8 | NP_004697.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152188Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00148 AC: 360AN: 242532Hom.: 2 AF XY: 0.00193 AC XY: 255AN XY: 132024
GnomAD4 exome AF: 0.000653 AC: 950AN: 1455364Hom.: 10 Cov.: 31 AF XY: 0.000910 AC XY: 659AN XY: 724294
GnomAD4 genome AF: 0.000282 AC: 43AN: 152306Hom.: 1 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:2
ARHGEF1: BP4, BS1, BS2 -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at