chr8-94494948-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_015496.5(VIRMA):c.4553A>T(p.Tyr1518Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000345 in 1,447,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y1518C) has been classified as Uncertain significance.
Frequency
Consequence
NM_015496.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIRMA | NM_015496.5 | c.4553A>T | p.Tyr1518Phe | missense_variant | 20/24 | ENST00000297591.10 | |
VIRMA | XM_047421677.1 | c.3548A>T | p.Tyr1183Phe | missense_variant | 21/25 | ||
VIRMA | XM_047421678.1 | c.3548A>T | p.Tyr1183Phe | missense_variant | 16/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIRMA | ENST00000297591.10 | c.4553A>T | p.Tyr1518Phe | missense_variant | 20/24 | 1 | NM_015496.5 | P1 | |
VIRMA | ENST00000522263.5 | c.*286A>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/15 | 1 | ||||
VIRMA | ENST00000521080.5 | n.5488+783A>T | intron_variant, non_coding_transcript_variant | 1 | |||||
VIRMA | ENST00000523263.1 | c.270+783A>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247166Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133558
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1447750Hom.: 0 Cov.: 26 AF XY: 0.00000139 AC XY: 1AN XY: 720910
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.4553A>T (p.Y1518F) alteration is located in exon 20 (coding exon 20) of the KIAA1429 gene. This alteration results from a A to T substitution at nucleotide position 4553, causing the tyrosine (Y) at amino acid position 1518 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