14-58347670-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002892.4(ARID4A):c.1196A>T(p.Tyr399Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,458,664 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002892.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID4A | NM_002892.4 | c.1196A>T | p.Tyr399Phe | missense_variant | Exon 15 of 24 | ENST00000355431.8 | NP_002883.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152224Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248296Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134616
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1458664Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 6AN XY: 725448
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1196A>T (p.Y399F) alteration is located in exon 15 (coding exon 14) of the ARID4A gene. This alteration results from a A to T substitution at nucleotide position 1196, causing the tyrosine (Y) at amino acid position 399 to be replaced by a phenylalanine (F). 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