12-108532330-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.1561C>T(p.His521Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,700 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.1561C>T | p.His521Tyr | missense_variant | 13/19 | ENST00000546815.6 | |
SART3 | NM_001410983.1 | c.1615C>T | p.His539Tyr | missense_variant | 13/19 | ||
SART3 | XM_047429916.1 | c.697C>T | p.His233Tyr | missense_variant | 8/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SART3 | ENST00000546815.6 | c.1561C>T | p.His521Tyr | missense_variant | 13/19 | 5 | NM_014706.4 | P1 | |
ENST00000662962.1 | n.165+92G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250552Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135466
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461496Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727032
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.1561C>T (p.H521Y) alteration is located in exon 13 (coding exon 13) of the SART3 gene. This alteration results from a C to T substitution at nucleotide position 1561, causing the histidine (H) at amino acid position 521 to be replaced by a tyrosine (Y). 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