rs1556181091
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_001555.5(IGSF1):c.2123_2149del(p.Ala708_Lys716del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 22)
Consequence
IGSF1
NM_001555.5 inframe_deletion
NM_001555.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.08
Genes affected
IGSF1 (HGNC:5948): (immunoglobulin superfamily member 1) This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001555.5.
PP5
Variant X-131278026-TCCTTATACAGAGCAAACCCCATGCCTG-T is Pathogenic according to our data. Variant chrX-131278026-TCCTTATACAGAGCAAACCCCATGCCTG-T is described in ClinVar as [Pathogenic]. Clinvar id is 39849.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-131278026-TCCTTATACAGAGCAAACCCCATGCCTG-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF1 | NM_001555.5 | c.2123_2149del | p.Ala708_Lys716del | inframe_deletion | 13/20 | ENST00000361420.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF1 | ENST00000361420.8 | c.2123_2149del | p.Ala708_Lys716del | inframe_deletion | 13/20 | 1 | NM_001555.5 | P4 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
X-linked central congenital hypothyroidism with late-onset testicular enlargement Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2012 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at