rs13796
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006118.4(HAX1):āc.159T>Cā(p.Ser53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,614,000 control chromosomes in the GnomAD database, including 13,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.096 ( 888 hom., cov: 31)
Exomes š: 0.13 ( 12565 hom. )
Consequence
HAX1
NM_006118.4 synonymous
NM_006118.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.348
Genes affected
HAX1 (HGNC:16915): (HCLS1 associated protein X-1) The protein encoded by this gene is known to associate with hematopoietic cell-specific Lyn substrate 1, a substrate of Src family tyrosine kinases. It also interacts with the product of the polycystic kidney disease 2 gene, mutations in which are associated with autosomal-dominant polycystic kidney disease, and with the F-actin-binding protein, cortactin. It was earlier thought that this gene product is mainly localized in the mitochondria, however, recent studies indicate it to be localized in the cell body. Mutations in this gene result in autosomal recessive severe congenital neutropenia, also known as Kostmann disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 1-154273441-T-C is Benign according to our data. Variant chr1-154273441-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 259917.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-154273441-T-C is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.348 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAX1 | NM_006118.4 | c.159T>C | p.Ser53= | synonymous_variant | 2/7 | ENST00000328703.12 | |
HAX1 | NM_001018837.2 | c.54-39T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAX1 | ENST00000328703.12 | c.159T>C | p.Ser53= | synonymous_variant | 2/7 | 1 | NM_006118.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0962 AC: 14635AN: 152062Hom.: 889 Cov.: 31
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GnomAD3 exomes AF: 0.116 AC: 29071AN: 251372Hom.: 1894 AF XY: 0.119 AC XY: 16112AN XY: 135876
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GnomAD4 exome AF: 0.127 AC: 186236AN: 1461820Hom.: 12565 Cov.: 34 AF XY: 0.128 AC XY: 93238AN XY: 727210
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GnomAD4 genome ? AF: 0.0962 AC: 14645AN: 152180Hom.: 888 Cov.: 31 AF XY: 0.0961 AC XY: 7153AN XY: 74414
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Kostmann syndrome Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 20, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Hereditary insensitivity to pain with anhidrosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 08, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at