1-153040264-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006945.5(SPRR2D):c.83C>T(p.Pro28Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,612,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006945.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPRR2D | ENST00000360379.4 | c.83C>T | p.Pro28Leu | missense_variant | Exon 2 of 2 | 1 | NM_006945.5 | ENSP00000353542.3 | ||
SPRR2D | ENST00000368756.1 | c.83C>T | p.Pro28Leu | missense_variant | Exon 3 of 3 | 2 | ENSP00000357745.1 | |||
SPRR2D | ENST00000368757.1 | c.83C>T | p.Pro28Leu | missense_variant | Exon 2 of 2 | 3 | ENSP00000357746.1 | |||
SPRR2D | ENST00000368758.3 | c.83C>T | p.Pro28Leu | missense_variant | Exon 2 of 2 | 2 | ENSP00000357747.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460280Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726442
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.83C>T (p.P28L) alteration is located in exon 2 (coding exon 1) of the SPRR2D gene. This alteration results from a C to T substitution at nucleotide position 83, causing the proline (P) at amino acid position 28 to be replaced by a leucine (L). 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