chr20-35174893-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006404.5(PROCR):āc.262T>Cā(p.Ser88Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000979 in 1,609,320 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_006404.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROCR | NM_006404.5 | c.262T>C | p.Ser88Pro | missense_variant | 2/4 | ENST00000216968.5 | |
MMP24-AS1-EDEM2 | NM_001355008.2 | c.-101-9022A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROCR | ENST00000216968.5 | c.262T>C | p.Ser88Pro | missense_variant | 2/4 | 1 | NM_006404.5 | P1 | |
ENST00000615962.1 | n.27A>G | non_coding_transcript_exon_variant | 1/1 | ||||||
PROCR | ENST00000635377.1 | c.163T>C | p.Ser55Pro | missense_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00108 AC: 164AN: 151332Hom.: 2 Cov.: 29
GnomAD3 exomes AF: 0.00186 AC: 444AN: 238974Hom.: 6 AF XY: 0.00188 AC XY: 244AN XY: 129768
GnomAD4 exome AF: 0.000968 AC: 1412AN: 1457988Hom.: 16 Cov.: 46 AF XY: 0.00106 AC XY: 765AN XY: 725096
GnomAD4 genome AF: 0.00108 AC: 164AN: 151332Hom.: 2 Cov.: 29 AF XY: 0.00118 AC XY: 87AN XY: 73848
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at