chr10-72062897-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001244950.2(SPOCK2):c.1138G>A(p.Val380Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000826 in 1,598,252 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001244950.2 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 | UniProt |
---|---|---|---|---|---|---|---|
SPOCK2 | NM_001244950.2 | c.1138G>A | p.Val380Met | missense_variant | 11/11 | ENST00000373109.7 | |
SPOCK2 | NM_014767.2 | c.1138G>A | p.Val380Met | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPOCK2 | ENST00000373109.7 | c.1138G>A | p.Val380Met | missense_variant | 11/11 | 1 | NM_001244950.2 | P1 | |
SPOCK2 | ENST00000317376.8 | c.1138G>A | p.Val380Met | missense_variant | 12/12 | 1 | P1 | ||
SPOCK2 | ENST00000463279.6 | n.706G>A | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
SPOCK2 | ENST00000469121.5 | n.774G>A | non_coding_transcript_exon_variant | 7/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152002Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000972 AC: 22AN: 226306Hom.: 0 AF XY: 0.000123 AC XY: 15AN XY: 122412
GnomAD4 exome AF: 0.0000802 AC: 116AN: 1446132Hom.: 1 Cov.: 74 AF XY: 0.0000752 AC XY: 54AN XY: 718490
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152120Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.1138G>A (p.V380M) alteration is located in exon 12 (coding exon 11) of the SPOCK2 gene. This alteration results from a G to A substitution at nucleotide position 1138, causing the valine (V) at amino acid position 380 to be replaced by a methionine (M). 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