12-108526433-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014706.4(SART3):c.2036C>T(p.Ser679Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SART3 | NM_014706.4 | c.2036C>T | p.Ser679Leu | missense_variant | 16/19 | ENST00000546815.6 | |
SART3 | NM_001410983.1 | c.2090C>T | p.Ser697Leu | missense_variant | 16/19 | ||
SART3 | XM_047429916.1 | c.1172C>T | p.Ser391Leu | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SART3 | ENST00000546815.6 | c.2036C>T | p.Ser679Leu | missense_variant | 16/19 | 5 | NM_014706.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251400Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135882
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461812Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727220
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.2036C>T (p.S679L) alteration is located in exon 16 (coding exon 16) of the SART3 gene. This alteration results from a C to T substitution at nucleotide position 2036, causing the serine (S) at amino acid position 679 to be replaced by a leucine (L). 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