chr7-142752957-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_Very_StrongBP7BS2_Supporting
The NM_002769.5(PRSS1):āc.681A>Gā(p.Gly227=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,926 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 Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. G227G) has been classified as Likely benign.
Frequency
Consequence
NM_002769.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS1 | NM_002769.5 | c.681A>G | p.Gly227= | synonymous_variant | 5/5 | ENST00000311737.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS1 | ENST00000311737.12 | c.681A>G | p.Gly227= | synonymous_variant | 5/5 | 1 | NM_002769.5 | P1 | |
PRSS1 | ENST00000486171.5 | c.723A>G | p.Gly241= | synonymous_variant | 6/6 | 5 | |||
PRSS1 | ENST00000492062.1 | c.*85A>G | 3_prime_UTR_variant | 4/4 | 2 | ||||
PRSS1 | ENST00000463701.1 | n.1145A>G | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 4AN: 151078Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251480Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135908
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461848Hom.: 0 Cov.: 50 AF XY: 0.0000124 AC XY: 9AN XY: 727236
GnomAD4 genome AF: 0.0000265 AC: 4AN: 151078Hom.: 0 Cov.: 28 AF XY: 0.0000135 AC XY: 1AN XY: 73802
ClinVar
Submissions by phenotype
Hereditary pancreatitis Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 16, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at