chr5-91371456-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020801.4(ARRDC3):āc.1189A>Gā(p.Ile397Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,612,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020801.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARRDC3 | NM_020801.4 | c.1189A>G | p.Ile397Val | missense_variant, splice_region_variant | 8/8 | ENST00000265138.4 | NP_065852.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARRDC3 | ENST00000265138.4 | c.1189A>G | p.Ile397Val | missense_variant, splice_region_variant | 8/8 | 1 | NM_020801.4 | ENSP00000265138 | P1 | |
ARRDC3 | ENST00000511391.1 | n.163A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250134Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135182
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460412Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 726514
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2022 | The c.1189A>G (p.I397V) alteration is located in exon 8 (coding exon 8) of the ARRDC3 gene. This alteration results from a A to G substitution at nucleotide position 1189, causing the isoleucine (I) at amino acid position 397 to be replaced by a valine (V). 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