chr5-62476703-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016338.5(IPO11):c.778A>G(p.Asn260Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00729 in 1,519,188 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_016338.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPO11 | NM_016338.5 | c.778A>G | p.Asn260Asp | missense_variant | 9/30 | ENST00000325324.11 | |
IPO11 | NM_001134779.2 | c.898A>G | p.Asn300Asp | missense_variant | 9/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO11 | ENST00000325324.11 | c.778A>G | p.Asn260Asp | missense_variant | 9/30 | 1 | NM_016338.5 | P1 | |
IPO11 | ENST00000409296.7 | c.898A>G | p.Asn300Asp | missense_variant | 9/30 | 2 | |||
IPO11 | ENST00000424533.5 | c.778A>G | p.Asn260Asp | missense_variant, NMD_transcript_variant | 9/29 | 2 | |||
IPO11 | ENST00000507640.1 | n.168+2239A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00643 AC: 979AN: 152206Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00630 AC: 1250AN: 198306Hom.: 7 AF XY: 0.00630 AC XY: 685AN XY: 108654
GnomAD4 exome AF: 0.00738 AC: 10090AN: 1366864Hom.: 45 Cov.: 28 AF XY: 0.00737 AC XY: 4993AN XY: 677794
GnomAD4 genome ? AF: 0.00643 AC: 979AN: 152324Hom.: 8 Cov.: 33 AF XY: 0.00610 AC XY: 454AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at