X-129919206-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006649.4(UTP14A):āc.569A>Gā(p.Asn190Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,209,435 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006649.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UTP14A | NM_006649.4 | c.569A>G | p.Asn190Ser | missense_variant | 7/15 | ENST00000394422.8 | NP_006640.2 | |
UTP14A | NM_001166221.2 | c.413A>G | p.Asn138Ser | missense_variant | 6/14 | NP_001159693.1 | ||
UTP14A | XM_047441790.1 | c.137A>G | p.Asn46Ser | missense_variant | 3/11 | XP_047297746.1 | ||
LOC105373335 | NR_188631.1 | n.218+10552T>C | intron_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000899 AC: 1AN: 111239Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33469
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183512Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67942
GnomAD4 exome AF: 0.0000127 AC: 14AN: 1098196Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 6AN XY: 363550
GnomAD4 genome AF: 0.00000899 AC: 1AN: 111239Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33469
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2024 | The c.569A>G (p.N190S) alteration is located in exon 7 (coding exon 7) of the UTP14A gene. This alteration results from a A to G substitution at nucleotide position 569, causing the asparagine (N) at amino acid position 190 to be replaced by a serine (S). 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