chr11-126406499-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001254757.2(ST3GAL4):āc.43C>Gā(p.Leu15Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,614,192 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001254757.2 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 | UniProt |
---|---|---|---|---|---|---|---|
ST3GAL4 | NM_001254757.2 | c.43C>G | p.Leu15Val | missense_variant | 3/11 | ENST00000444328.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST3GAL4 | ENST00000444328.7 | c.43C>G | p.Leu15Val | missense_variant | 3/11 | 5 | NM_001254757.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251456Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135900
GnomAD4 exome AF: 0.000165 AC: 241AN: 1461878Hom.: 3 Cov.: 34 AF XY: 0.000190 AC XY: 138AN XY: 727242
GnomAD4 genome AF: 0.000151 AC: 23AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.43C>G (p.L15V) alteration is located in exon 3 (coding exon 2) of the ST3GAL4 gene. This alteration results from a C to G substitution at nucleotide position 43, causing the leucine (L) at amino acid position 15 to be replaced by a valine (V). 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