7-142749475-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_002769.5(PRSS1):c.-10C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002769.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS1 | ENST00000311737 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_002769.5 | ENSP00000308720.7 | |||
PRSS1 | ENST00000486171 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 6 | 5 | ENSP00000417854.1 | ||||
PRSS1 | ENST00000485223.1 | n.4C>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
PRSS1 | ENST00000497041.1 | n.-6C>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152160Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251480Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135910
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461824Hom.: 0 Cov.: 47 AF XY: 0.0000138 AC XY: 10AN XY: 727212
GnomAD4 genome AF: 0.000138 AC: 21AN: 152160Hom.: 0 Cov.: 34 AF XY: 0.000175 AC XY: 13AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: PRSS1 c.-10C>A is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 3.6e-05 in 251480 control chromosomes, predominantly at a frequency of 0.00055 within the African or African-American subpopulation in the gnomAD database. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-10C>A in individuals affected with Chronic Pancreatitis Risk and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 2445752). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at