1-153040177-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006945.5(SPRR2D):c.170T>G(p.Val57Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,612,990 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.170T>G | p.Val57Gly | missense_variant | Exon 2 of 2 | 1 | NM_006945.5 | ENSP00000353542.3 | ||
SPRR2D | ENST00000368756.1 | c.170T>G | p.Val57Gly | missense_variant | Exon 3 of 3 | 2 | ENSP00000357745.1 | |||
SPRR2D | ENST00000368757.1 | c.170T>G | p.Val57Gly | missense_variant | Exon 2 of 2 | 3 | ENSP00000357746.1 | |||
SPRR2D | ENST00000368758.3 | c.170T>G | p.Val57Gly | missense_variant | Exon 2 of 2 | 2 | ENSP00000357747.3 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251116Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135698
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1460762Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 726724
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.170T>G (p.V57G) alteration is located in exon 2 (coding exon 1) of the SPRR2D gene. This alteration results from a T to G substitution at nucleotide position 170, causing the valine (V) at amino acid position 57 to be replaced by a glycine (G). 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