chr1-160093022-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052868.6(IGSF8):c.1214G>A(p.Arg405His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R405C) has been classified as Uncertain significance.
Frequency
Consequence
NM_052868.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF8 | NM_052868.6 | c.1214G>A | p.Arg405His | missense_variant | 4/7 | ENST00000314485.12 | NP_443100.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGSF8 | ENST00000314485.12 | c.1214G>A | p.Arg405His | missense_variant | 4/7 | 1 | NM_052868.6 | ENSP00000316664.7 | ||
IGSF8 | ENST00000368086.5 | c.1214G>A | p.Arg405His | missense_variant | 4/7 | 1 | ENSP00000357065.1 | |||
IGSF8 | ENST00000614243.4 | c.1214G>A | p.Arg405His | missense_variant | 5/8 | 1 | ENSP00000477565.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250718Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135654
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461788Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 727200
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2021 | The c.1214G>A (p.R405H) alteration is located in exon 4 (coding exon 4) of the IGSF8 gene. This alteration results from a G to A substitution at nucleotide position 1214, causing the arginine (R) at amino acid position 405 to be replaced by a histidine (H). 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