chr4-87982622-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040058.2(SPP1):c.671G>A(p.Ser224Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00824 in 1,614,054 control chromosomes in the GnomAD database, including 918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001040058.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPP1 | NM_001040058.2 | c.671G>A | p.Ser224Asn | missense_variant | 7/7 | ENST00000395080.8 | NP_001035147.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPP1 | ENST00000395080.8 | c.671G>A | p.Ser224Asn | missense_variant | 7/7 | 1 | NM_001040058.2 | ENSP00000378517.3 |
Frequencies
GnomAD3 genomes AF: 0.0434 AC: 6597AN: 152046Hom.: 489 Cov.: 32
GnomAD3 exomes AF: 0.0116 AC: 2910AN: 251480Hom.: 189 AF XY: 0.00834 AC XY: 1133AN XY: 135912
GnomAD4 exome AF: 0.00458 AC: 6689AN: 1461890Hom.: 430 Cov.: 30 AF XY: 0.00396 AC XY: 2883AN XY: 727246
GnomAD4 genome AF: 0.0434 AC: 6608AN: 152164Hom.: 488 Cov.: 32 AF XY: 0.0421 AC XY: 3134AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at