X-66032493-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_007268.3(VSIG4):c.669C>A(p.Ser223Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,209,749 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S223S) has been classified as Likely benign.
Frequency
Consequence
NM_007268.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSIG4 | NM_007268.3 | c.669C>A | p.Ser223Arg | missense_variant | 3/8 | ENST00000374737.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSIG4 | ENST00000374737.9 | c.669C>A | p.Ser223Arg | missense_variant | 3/8 | 1 | NM_007268.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112141Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34313
GnomAD3 exomes AF: 0.0000602 AC: 11AN: 182611Hom.: 0 AF XY: 0.0000446 AC XY: 3AN XY: 67287
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1097608Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 8AN XY: 363100
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112141Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34313
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.669C>A (p.S223R) alteration is located in exon 3 (coding exon 3) of the VSIG4 gene. This alteration results from a C to A substitution at nucleotide position 669, causing the serine (S) at amino acid position 223 to be replaced by an arginine (R). 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