8-94492748-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015496.5(VIRMA):c.4712G>A(p.Arg1571His) variant causes a missense change. The variant allele was found at a frequency of 0.000117 in 1,613,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015496.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VIRMA | NM_015496.5 | c.4712G>A | p.Arg1571His | missense_variant | Exon 21 of 24 | ENST00000297591.10 | NP_056311.2 | |
VIRMA | XM_047421677.1 | c.3707G>A | p.Arg1236His | missense_variant | Exon 22 of 25 | XP_047277633.1 | ||
VIRMA | XM_047421678.1 | c.3707G>A | p.Arg1236His | missense_variant | Exon 17 of 20 | XP_047277634.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251266Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135812
GnomAD4 exome AF: 0.000123 AC: 180AN: 1461624Hom.: 0 Cov.: 30 AF XY: 0.000131 AC XY: 95AN XY: 727132
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4712G>A (p.R1571H) alteration is located in exon 21 (coding exon 21) of the KIAA1429 gene. This alteration results from a G to A substitution at nucleotide position 4712, causing the arginine (R) at amino acid position 1571 to be replaced by a histidine (H). 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