chrX-131273901-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001555.5(IGSF1):c.3906C>G(p.Thr1302=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,208,539 control chromosomes in the GnomAD database, including 1 homozygotes. There are 98 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0015 ( 0 hom., 53 hem., cov: 22)
Exomes 𝑓: 0.00017 ( 1 hom. 45 hem. )
Consequence
IGSF1
NM_001555.5 synonymous
NM_001555.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.362
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant X-131273901-G-C is Benign according to our data. Variant chrX-131273901-G-C is described in ClinVar as [Benign]. Clinvar id is 1284299.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-131273901-G-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.362 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00154 (172/111469) while in subpopulation AFR AF= 0.00536 (164/30614). AF 95% confidence interval is 0.00469. There are 0 homozygotes in gnomad4. There are 53 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd at 53 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF1 | NM_001555.5 | c.3906C>G | p.Thr1302= | synonymous_variant | 20/20 | ENST00000361420.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF1 | ENST00000361420.8 | c.3906C>G | p.Thr1302= | synonymous_variant | 20/20 | 1 | NM_001555.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00154 AC: 172AN: 111413Hom.: 0 Cov.: 22 AF XY: 0.00158 AC XY: 53AN XY: 33595
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GnomAD3 exomes AF: 0.000514 AC: 94AN: 182883Hom.: 1 AF XY: 0.000371 AC XY: 25AN XY: 67357
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GnomAD4 exome AF: 0.000173 AC: 190AN: 1097070Hom.: 1 Cov.: 30 AF XY: 0.000124 AC XY: 45AN XY: 362452
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at