chr5-62451933-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_016338.5(IPO11):āc.516T>Cā(p.Asp172=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000172 in 1,608,944 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_016338.5 splice_region, synonymous
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 |
---|---|---|---|---|---|---|---|
IPO11 | NM_016338.5 | c.516T>C | p.Asp172= | splice_region_variant, synonymous_variant | 5/30 | ENST00000325324.11 | |
IPO11 | NM_001134779.2 | c.636T>C | p.Asp212= | splice_region_variant, synonymous_variant | 5/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO11 | ENST00000325324.11 | c.516T>C | p.Asp172= | splice_region_variant, synonymous_variant | 5/30 | 1 | NM_016338.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000828 AC: 126AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251148Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135738
GnomAD4 exome AF: 0.000101 AC: 147AN: 1456586Hom.: 1 Cov.: 29 AF XY: 0.0000759 AC XY: 55AN XY: 724996
GnomAD4 genome AF: 0.000853 AC: 130AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at