15-39588617-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_003246.4(THBS1):c.1563C>T(p.Asn521Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0293 in 1,611,476 control chromosomes in the GnomAD database, including 790 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003246.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THBS1 | NM_003246.4 | c.1563C>T | p.Asn521Asn | synonymous_variant | Exon 10 of 22 | ENST00000260356.6 | NP_003237.2 | |
THBS1 | XM_047432980.1 | c.1563C>T | p.Asn521Asn | synonymous_variant | Exon 10 of 22 | XP_047288936.1 | ||
THBS1 | XM_011521971.3 | c.1472-342C>T | intron_variant | Intron 9 of 20 | XP_011520273.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THBS1 | ENST00000260356.6 | c.1563C>T | p.Asn521Asn | synonymous_variant | Exon 10 of 22 | 1 | NM_003246.4 | ENSP00000260356.5 | ||
THBS1 | ENST00000497720.1 | n.359C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
THBS1-AS1 | ENST00000616754.1 | n.266G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 | |||||
FSIP1 | ENST00000642527.1 | n.*215-43G>A | intron_variant | Intron 3 of 3 | ENSP00000496642.1 |
Frequencies
GnomAD3 genomes AF: 0.0221 AC: 3368AN: 152158Hom.: 68 Cov.: 32
GnomAD3 exomes AF: 0.0238 AC: 5918AN: 248838Hom.: 97 AF XY: 0.0245 AC XY: 3295AN XY: 134470
GnomAD4 exome AF: 0.0301 AC: 43886AN: 1459200Hom.: 722 Cov.: 31 AF XY: 0.0300 AC XY: 21764AN XY: 725820
GnomAD4 genome AF: 0.0221 AC: 3369AN: 152276Hom.: 68 Cov.: 32 AF XY: 0.0206 AC XY: 1531AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent, not in splice consensus -
not provided Benign:1
- -
THBS1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at