2-96551439-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_212481.3(ARID5A):c.911T>C(p.Leu304Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,596,498 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_212481.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID5A | NM_212481.3 | c.911T>C | p.Leu304Pro | missense_variant | 7/7 | ENST00000357485.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID5A | ENST00000357485.8 | c.911T>C | p.Leu304Pro | missense_variant | 7/7 | 1 | NM_212481.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000913 AC: 139AN: 152198Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000171 AC: 36AN: 210480Hom.: 1 AF XY: 0.000121 AC XY: 14AN XY: 115810
GnomAD4 exome AF: 0.0000859 AC: 124AN: 1444182Hom.: 0 Cov.: 31 AF XY: 0.0000641 AC XY: 46AN XY: 717382
GnomAD4 genome ? AF: 0.000919 AC: 140AN: 152316Hom.: 2 Cov.: 33 AF XY: 0.000967 AC XY: 72AN XY: 74476
ClinVar
Submissions by phenotype
ARID5A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 17, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at