9-93075873-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145006.4(SUSD3):c.178C>T(p.Arg60Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000521 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145006.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUSD3 | ENST00000375472.8 | c.178C>T | p.Arg60Cys | missense_variant | Exon 2 of 5 | 1 | NM_145006.4 | ENSP00000364621.3 | ||
SUSD3 | ENST00000375469.5 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 5 | 5 | ENSP00000364618.1 | |||
SUSD3 | ENST00000617293.4 | c.178C>T | p.Arg60Cys | missense_variant | Exon 2 of 4 | 3 | ENSP00000479555.1 | |||
SUSD3 | ENST00000465709.5 | c.53-1973C>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000475051.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152058Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251178Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135806
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461774Hom.: 0 Cov.: 34 AF XY: 0.0000481 AC XY: 35AN XY: 727194
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152058Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.178C>T (p.R60C) alteration is located in exon 2 (coding exon 2) of the SUSD3 gene. This alteration results from a C to T substitution at nucleotide position 178, causing the arginine (R) at amino acid position 60 to be replaced by a cysteine (C). 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