rs7435825
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000395080.8(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
ENST00000395080.8 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 | P1 | |
ENST00000662475.1 | n.307+6736C>T | intron_variant, non_coding_transcript_variant |
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