chr4-105655699-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242729.2(ARHGEF38):c.1210G>A(p.Ala404Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000073 in 1,535,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001242729.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF38 | NM_001242729.2 | c.1210G>A | p.Ala404Thr | missense_variant | 9/14 | ENST00000420470.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF38 | ENST00000420470.3 | c.1210G>A | p.Ala404Thr | missense_variant | 9/14 | 5 | NM_001242729.2 | P1 | |
ARHGEF38 | ENST00000508036.2 | n.910G>A | non_coding_transcript_exon_variant | 6/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 22AN: 137134Hom.: 0 AF XY: 0.000107 AC XY: 8AN XY: 74446
GnomAD4 exome AF: 0.0000759 AC: 105AN: 1382916Hom.: 0 Cov.: 30 AF XY: 0.0000703 AC XY: 48AN XY: 682386
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.1210G>A (p.A404T) alteration is located in exon 9 (coding exon 9) of the ARHGEF38 gene. This alteration results from a G to A substitution at nucleotide position 1210, causing the alanine (A) at amino acid position 404 to be replaced by a threonine (T). 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