rs1132785
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_198682.3(GYPE):āc.38G>Cā(p.Gly13Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G13E) has been classified as Likely benign.
Frequency
Consequence
NM_198682.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYPE | NM_198682.3 | c.38G>C | p.Gly13Ala | missense_variant, splice_region_variant | 2/4 | ENST00000358615.9 | |
LOC105377459 | XR_001741861.1 | n.1463+14433C>G | intron_variant, non_coding_transcript_variant | ||||
GYPE | NM_002102.4 | c.38G>C | p.Gly13Ala | missense_variant, splice_region_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYPE | ENST00000358615.9 | c.38G>C | p.Gly13Ala | missense_variant, splice_region_variant | 2/4 | 1 | NM_198682.3 | P1 | |
GUSBP5 | ENST00000641328.1 | n.1315+14433C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 39796AN: 132948Hom.: 4 Cov.: 43 FAILED QC
GnomAD3 exomes AF: 0.262 AC: 54614AN: 208744Hom.: 1 AF XY: 0.263 AC XY: 29750AN XY: 113244
GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.306 AC: 415445AN: 1355624Hom.: 5 Cov.: 83 AF XY: 0.309 AC XY: 208690AN XY: 675718
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.299 AC: 39829AN: 133042Hom.: 4 Cov.: 43 AF XY: 0.306 AC XY: 19877AN XY: 64958
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency (no homozygotes in ExAC) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at