1-53883208-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018982.5(YIPF1):āc.100G>Cā(p.Gly34Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000415 in 1,445,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018982.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF1 | NM_018982.5 | c.100G>C | p.Gly34Arg | missense_variant | 4/11 | ENST00000072644.7 | |
YIPF1 | NR_036639.2 | n.454G>C | non_coding_transcript_exon_variant | 4/12 | |||
YIPF1 | NR_036640.2 | n.234G>C | non_coding_transcript_exon_variant | 3/11 | |||
YIPF1 | NR_135075.2 | n.154G>C | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF1 | ENST00000072644.7 | c.100G>C | p.Gly34Arg | missense_variant | 4/11 | 1 | NM_018982.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000423 AC: 1AN: 236316Hom.: 0 AF XY: 0.00000781 AC XY: 1AN XY: 128024
GnomAD4 exome AF: 0.00000415 AC: 6AN: 1445460Hom.: 0 Cov.: 30 AF XY: 0.00000417 AC XY: 3AN XY: 718732
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.100G>C (p.G34R) alteration is located in exon 4 (coding exon 2) of the YIPF1 gene. This alteration results from a G to C substitution at nucleotide position 100, causing the glycine (G) at amino acid position 34 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at