chr4-166742020-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040159.2(SPOCK3):c.971G>A(p.Arg324Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,612,770 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040159.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPOCK3 | NM_001040159.2 | c.971G>A | p.Arg324Gln | missense_variant | 9/11 | ENST00000357545.9 | NP_001035249.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPOCK3 | ENST00000357545.9 | c.971G>A | p.Arg324Gln | missense_variant | 9/11 | 1 | NM_001040159.2 | ENSP00000350153 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 151996Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000211 AC: 53AN: 250896Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135596
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1460658Hom.: 0 Cov.: 29 AF XY: 0.0000839 AC XY: 61AN XY: 726698
GnomAD4 genome AF: 0.000105 AC: 16AN: 152112Hom.: 1 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.980G>A (p.R327Q) alteration is located in exon 10 (coding exon 9) of the SPOCK3 gene. This alteration results from a G to A substitution at nucleotide position 980, causing the arginine (R) at amino acid position 327 to be replaced by a glutamine (Q). 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