chrX-131275095-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001555.5(IGSF1):c.3376G>A(p.Gly1126Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000881 in 1,209,191 control chromosomes in the GnomAD database, including 6 homozygotes. There are 275 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001555.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF1 | NM_001555.5 | c.3376G>A | p.Gly1126Ser | missense_variant | 17/20 | ENST00000361420.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF1 | ENST00000361420.8 | c.3376G>A | p.Gly1126Ser | missense_variant | 17/20 | 1 | NM_001555.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00477 AC: 533AN: 111781Hom.: 4 Cov.: 23 AF XY: 0.00436 AC XY: 148AN XY: 33941
GnomAD3 exomes AF: 0.00148 AC: 271AN: 183464Hom.: 2 AF XY: 0.00100 AC XY: 68AN XY: 67898
GnomAD4 exome AF: 0.000485 AC: 532AN: 1097356Hom.: 2 Cov.: 32 AF XY: 0.000347 AC XY: 126AN XY: 362718
GnomAD4 genome ? AF: 0.00477 AC: 533AN: 111835Hom.: 4 Cov.: 23 AF XY: 0.00438 AC XY: 149AN XY: 34005
ClinVar
Submissions by phenotype
IGSF1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at