1-153003830-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000295367.5(SPRR3):c.*300T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 438,488 control chromosomes in the GnomAD database, including 64,140 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.
Frequency
Genomes: 𝑓 0.53 ( 21531 hom., cov: 32)
Exomes 𝑓: 0.54 ( 42609 hom. )
Consequence
SPRR3
ENST00000295367.5 3_prime_UTR
ENST00000295367.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.00
Genes affected
SPRR3 (HGNC:11268): (small proline rich protein 3) Predicted to enable structural molecule activity. Predicted to be involved in wound healing. Located in Golgi apparatus and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPRR3 | NM_001097589.2 | c.*300T>G | 3_prime_UTR_variant | 2/2 | ENST00000295367.5 | NP_001091058.1 | ||
SPRR3 | NM_005416.3 | c.*300T>G | 3_prime_UTR_variant | 3/3 | NP_005407.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPRR3 | ENST00000295367.5 | c.*300T>G | 3_prime_UTR_variant | 2/2 | 1 | NM_001097589.2 | ENSP00000295367 | P1 | ||
SPRR3 | ENST00000331860.7 | c.*300T>G | 3_prime_UTR_variant | 3/3 | 3 | ENSP00000330391 | P1 |
Frequencies
GnomAD3 genomes AF: 0.530 AC: 80565AN: 151900Hom.: 21505 Cov.: 32
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GnomAD4 exome AF: 0.539 AC: 154537AN: 286470Hom.: 42609 Cov.: 3 AF XY: 0.540 AC XY: 80085AN XY: 148392
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GnomAD4 genome AF: 0.530 AC: 80643AN: 152018Hom.: 21531 Cov.: 32 AF XY: 0.527 AC XY: 39181AN XY: 74332
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at