12-108523563-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014706.4(SART3):c.2786A>G(p.Gln929Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000201 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014706.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SART3 | NM_014706.4 | c.2786A>G | p.Gln929Arg | missense_variant | Exon 19 of 19 | ENST00000546815.6 | NP_055521.1 | |
SART3 | NM_001410983.1 | c.2840A>G | p.Gln947Arg | missense_variant | Exon 19 of 19 | NP_001397912.1 | ||
SART3 | XM_047429916.1 | c.1922A>G | p.Gln641Arg | missense_variant | Exon 14 of 14 | XP_047285872.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251318Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135864
GnomAD4 exome AF: 0.000205 AC: 300AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.000194 AC XY: 141AN XY: 727234
GnomAD4 genome AF: 0.000164 AC: 25AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2786A>G (p.Q929R) alteration is located in exon 19 (coding exon 19) of the SART3 gene. This alteration results from a A to G substitution at nucleotide position 2786, causing the glutamine (Q) at amino acid position 929 to be replaced by an arginine (R). 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