3-33153422-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015551.2(SUSD5):āc.1210A>Cā(p.Asn404His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015551.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUSD5 | NM_015551.2 | c.1210A>C | p.Asn404His | missense_variant | 5/5 | ENST00000309558.8 | |
SUSD5 | XM_005265034.4 | c.1021A>C | p.Asn341His | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUSD5 | ENST00000309558.8 | c.1210A>C | p.Asn404His | missense_variant | 5/5 | 1 | NM_015551.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248596Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134840
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461622Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727050
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 30, 2023 | The c.1210A>C (p.N404H) alteration is located in exon 5 (coding exon 5) of the SUSD5 gene. This alteration results from a A to C substitution at nucleotide position 1210, causing the asparagine (N) at amino acid position 404 to be replaced by a histidine (H). 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