chr12-45852423-G-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_152641.4(ARID2):c.4300G>T(p.Ala1434Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,614,122 control chromosomes in the GnomAD database, including 146 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_152641.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID2 | NM_152641.4 | c.4300G>T | p.Ala1434Ser | missense_variant | 15/21 | ENST00000334344.11 | |
ARID2 | NM_001347839.2 | c.4300G>T | p.Ala1434Ser | missense_variant | 15/20 | ||
ARID2 | XM_047428489.1 | c.4300G>T | p.Ala1434Ser | missense_variant | 15/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID2 | ENST00000334344.11 | c.4300G>T | p.Ala1434Ser | missense_variant | 15/21 | 1 | NM_152641.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00325 AC: 494AN: 152148Hom.: 18 Cov.: 32
GnomAD3 exomes AF: 0.00658 AC: 1653AN: 251152Hom.: 66 AF XY: 0.00592 AC XY: 804AN XY: 135740
GnomAD4 exome AF: 0.00230 AC: 3365AN: 1461856Hom.: 128 Cov.: 32 AF XY: 0.00222 AC XY: 1617AN XY: 727232
GnomAD4 genome AF: 0.00323 AC: 492AN: 152266Hom.: 18 Cov.: 32 AF XY: 0.00339 AC XY: 252AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
ARID2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 15, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Coffin-Siris syndrome 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 19, 2021 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at