rs1053839
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178483.3(SCP2D1):c.295C>T(p.Pro99Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,613,460 control chromosomes in the GnomAD database, including 31,134 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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_178483.3 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 | UniProt |
---|---|---|---|---|---|---|---|
SCP2D1 | NM_178483.3 | c.295C>T | p.Pro99Ser | missense_variant | 1/1 | ENST00000377428.4 | |
SCP2D1-AS1 | NR_161343.1 | n.245-3995G>A | intron_variant, non_coding_transcript_variant | ||||
SCP2D1-AS1 | NR_161342.1 | n.269-3995G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCP2D1 | ENST00000377428.4 | c.295C>T | p.Pro99Ser | missense_variant | 1/1 | NM_178483.3 | P1 | ||
SCP2D1-AS1 | ENST00000623418.1 | n.219-3995G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.233 AC: 35363AN: 151940Hom.: 5033 Cov.: 32
GnomAD3 exomes AF: 0.185 AC: 46480AN: 251374Hom.: 5018 AF XY: 0.185 AC XY: 25093AN XY: 135862
GnomAD4 exome AF: 0.183 AC: 267429AN: 1461402Hom.: 26093 Cov.: 33 AF XY: 0.184 AC XY: 134001AN XY: 727034
GnomAD4 genome ? AF: 0.233 AC: 35412AN: 152058Hom.: 5041 Cov.: 32 AF XY: 0.232 AC XY: 17233AN XY: 74338
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at