rs781808414
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BP6BS2
The NM_001111125.3(IQSEC2):c.2831A>G(p.Asn944Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000206 in 1,165,804 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. N944N) has been classified as Benign.
Frequency
Consequence
NM_001111125.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.2831A>G | p.Asn944Ser | missense_variant | 9/15 | ENST00000642864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.2831A>G | p.Asn944Ser | missense_variant | 9/15 | NM_001111125.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000181 AC: 2AN: 110574Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32810
GnomAD3 exomes AF: 0.0000772 AC: 9AN: 116509Hom.: 0 AF XY: 0.0000738 AC XY: 3AN XY: 40643
GnomAD4 exome AF: 0.0000208 AC: 22AN: 1055230Hom.: 0 Cov.: 30 AF XY: 0.0000145 AC XY: 5AN XY: 345126
GnomAD4 genome ? AF: 0.0000181 AC: 2AN: 110574Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32810
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.2831A>G (p.N944S) alteration is located in exon 9 (coding exon 9) of the IQSEC2 gene. This alteration results from a A to G substitution at nucleotide position 2831, causing the asparagine (N) at amino acid position 944 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Intellectual disability, X-linked 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 03, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at