16-21641543-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005849.4(IGSF6):c.717A>T(p.Glu239Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000315 in 1,585,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005849.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF6 | NM_005849.4 | c.717A>T | p.Glu239Asp | missense_variant | 6/6 | ENST00000268389.6 | |
METTL9 | NM_016025.5 | c.752-13684T>A | intron_variant | ENST00000358154.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF6 | ENST00000268389.6 | c.717A>T | p.Glu239Asp | missense_variant | 6/6 | 1 | NM_005849.4 | P1 | |
METTL9 | ENST00000358154.8 | c.752-13684T>A | intron_variant | 1 | NM_016025.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245178Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132648
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1433762Hom.: 0 Cov.: 25 AF XY: 0.00000280 AC XY: 2AN XY: 714612
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at