4-1170414-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012445.4(SPON2):c.799G>A(p.Asp267Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012445.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPON2 | NM_012445.4 | c.799G>A | p.Asp267Asn | missense_variant | Exon 5 of 6 | ENST00000290902.10 | NP_036577.2 | |
SPON2 | NM_001128325.3 | c.799G>A | p.Asp267Asn | missense_variant | Exon 6 of 7 | NP_001121797.2 | ||
SPON2 | NM_001199021.2 | c.799G>A | p.Asp267Asn | missense_variant | Exon 7 of 8 | NP_001185950.2 | ||
LOC124900647 | XM_047416477.1 | c.-2486-20686C>T | intron_variant | Intron 1 of 2 | XP_047272433.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPON2 | ENST00000290902.10 | c.799G>A | p.Asp267Asn | missense_variant | Exon 5 of 6 | 1 | NM_012445.4 | ENSP00000290902.5 | ||
SPON2 | ENST00000431380.5 | c.799G>A | p.Asp267Asn | missense_variant | Exon 6 of 7 | 5 | ENSP00000394832.1 | |||
SPON2 | ENST00000617421.4 | c.799G>A | p.Asp267Asn | missense_variant | Exon 7 of 8 | 5 | ENSP00000483599.1 | |||
SPON2 | ENST00000509697.1 | n.235G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249346Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134860
GnomAD4 exome AF: 0.0000500 AC: 73AN: 1461158Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 726872
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.799G>A (p.D267N) alteration is located in exon 7 (coding exon 4) of the SPON2 gene. This alteration results from a G to A substitution at nucleotide position 799, causing the aspartic acid (D) at amino acid position 267 to be replaced by an asparagine (N). 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