X-129911796-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000394422.8(UTP14A):c.412G>A(p.Ala138Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000265 in 1,208,916 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000394422.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UTP14A | NM_006649.4 | c.412G>A | p.Ala138Thr | missense_variant | 6/15 | ENST00000394422.8 | NP_006640.2 | |
LOC105373335 | XR_007068332.1 | n.1774-2853C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UTP14A | ENST00000394422.8 | c.412G>A | p.Ala138Thr | missense_variant | 6/15 | 1 | NM_006649.4 | ENSP00000377944 | P1 | |
ENST00000432062.1 | n.207-3243C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000270 AC: 3AN: 111063Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33287
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183331Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67779
GnomAD4 exome AF: 0.0000264 AC: 29AN: 1097853Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 11AN XY: 363227
GnomAD4 genome AF: 0.0000270 AC: 3AN: 111063Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33287
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.412G>A (p.A138T) alteration is located in exon 6 (coding exon 6) of the UTP14A gene. This alteration results from a G to A substitution at nucleotide position 412, causing the alanine (A) at amino acid position 138 to be replaced by a threonine (T). 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