9-112078622-G-A
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_022486.5(SUSD1):c.1669C>T(p.Arg557Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022486.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUSD1 | ENST00000374270.8 | c.1669C>T | p.Arg557Cys | missense_variant | Exon 12 of 17 | 1 | NM_022486.5 | ENSP00000363388.4 | ||
SUSD1 | ENST00000374264.6 | c.1669C>T | p.Arg557Cys | missense_variant | Exon 12 of 18 | 1 | ENSP00000363382.2 | |||
SUSD1 | ENST00000374263.7 | c.1669C>T | p.Arg557Cys | missense_variant | Exon 12 of 16 | 2 | ENSP00000363381.3 | |||
SUSD1 | ENST00000355396.7 | c.1618C>T | p.Arg540Cys | missense_variant | Exon 12 of 16 | 2 | ENSP00000347558.3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152138Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.000111 AC: 28AN: 251444 AF XY: 0.000155 show subpopulations
GnomAD4 exome AF: 0.0000465 AC: 68AN: 1461812Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727204 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152138Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74326 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1669C>T (p.R557C) alteration is located in exon 12 (coding exon 12) of the SUSD1 gene. This alteration results from a C to T substitution at nucleotide position 1669, causing the arginine (R) at amino acid position 557 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