5-141656242-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022481.6(ARAP3):c.3824G>A(p.Gly1275Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022481.6 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARAP3 | NM_022481.6 | c.3824G>A | p.Gly1275Asp | missense_variant | 28/33 | ENST00000239440.9 | NP_071926.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARAP3 | ENST00000239440.9 | c.3824G>A | p.Gly1275Asp | missense_variant | 28/33 | 1 | NM_022481.6 | ENSP00000239440 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251300Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135838
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461888Hom.: 0 Cov.: 35 AF XY: 0.00000963 AC XY: 7AN XY: 727246
GnomAD4 genome AF: 0.000164 AC: 25AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.3824G>A (p.G1275D) alteration is located in exon 28 (coding exon 27) of the ARAP3 gene. This alteration results from a G to A substitution at nucleotide position 3824, causing the glycine (G) at amino acid position 1275 to be replaced by an aspartic acid (D). 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