19-40381092-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144685.5(HIPK4):c.899C>A(p.Ala300Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,611,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144685.5 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 |
---|---|---|---|---|---|---|---|
HIPK4 | NM_144685.5 | c.899C>A | p.Ala300Asp | missense_variant | 3/4 | ENST00000291823.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIPK4 | ENST00000291823.3 | c.899C>A | p.Ala300Asp | missense_variant | 3/4 | 1 | NM_144685.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1459224Hom.: 0 Cov.: 33 AF XY: 0.0000207 AC XY: 15AN XY: 726024
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152380Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | The c.899C>A (p.A300D) alteration is located in exon 3 (coding exon 3) of the HIPK4 gene. This alteration results from a C to A substitution at nucleotide position 899, causing the alanine (A) at amino acid position 300 to be replaced by an aspartic acid (D). 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