rs117160567
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000520.6(HEXA):c.672+30T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 1,390,626 control chromosomes in the GnomAD database, including 478 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 40 hom., cov: 32)
Exomes 𝑓: 0.024 ( 438 hom. )
Consequence
HEXA
NM_000520.6 intron
NM_000520.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.261
Genes affected
HEXA (HGNC:4878): (hexosaminidase subunit alpha) This gene encodes a member of the glycosyl hydrolase 20 family of proteins. The encoded preproprotein is proteolytically processed to generate the alpha subunit of the lysosomal enzyme beta-hexosaminidase. This enzyme, together with the cofactor GM2 activator protein, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Mutations in this gene lead to an accumulation of GM2 ganglioside in neurons, the underlying cause of neurodegenerative disorders termed the GM2 gangliosidoses, including Tay-Sachs disease (GM2-gangliosidosis type I). Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 15-72351103-A-C is Benign according to our data. Variant chr15-72351103-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 256351.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-72351103-A-C is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.016 (2435/152290) while in subpopulation SAS AF= 0.0494 (238/4822). AF 95% confidence interval is 0.0442. There are 40 homozygotes in gnomad4. There are 1172 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 40 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEXA | NM_000520.6 | c.672+30T>G | intron_variant | ENST00000268097.10 | |||
HEXA | NM_001318825.2 | c.705+30T>G | intron_variant | ||||
HEXA | NR_134869.3 | n.714+30T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEXA | ENST00000268097.10 | c.672+30T>G | intron_variant | 1 | NM_000520.6 | P1 | |||
ENST00000570175.1 | n.2457A>C | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0160 AC: 2433AN: 152172Hom.: 39 Cov.: 32
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GnomAD3 exomes AF: 0.0191 AC: 4791AN: 250938Hom.: 87 AF XY: 0.0217 AC XY: 2943AN XY: 135610
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GnomAD4 exome AF: 0.0236 AC: 29195AN: 1238336Hom.: 438 Cov.: 18 AF XY: 0.0247 AC XY: 15493AN XY: 627650
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GnomAD4 genome ? AF: 0.0160 AC: 2435AN: 152290Hom.: 40 Cov.: 32 AF XY: 0.0157 AC XY: 1172AN XY: 74478
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Pathogenic:1Benign:11
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Tay-Sachs disease Pathogenic:1Benign:4
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jun 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | May 04, 2023 | South Asian population allele frequency is 4.368% (rs117160567, 1395/30540 alleles, 49 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.3.2, this variant is classified as BENIGN. Following criteria are met: BA1 - |
Benign, criteria provided, single submitter | research | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | - | The c.672+30T>G variant in HEXA has been identified in at least 1 Tay-Sachs disease carrier (PMID: 7717398), and has been identified in >4% of South Asian chromosomes and 43 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for Tay-Sachs disease. - |
Pathogenic, no assertion criteria provided | research | Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics | Mar 22, 2011 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:5
Benign, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The HEXA c.705+30T>G variant was not identified in the ClinVar, Cosmic, MutDB or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs117160567) and in control databases in 5209 of 282340 chromosomes (93 homozygous) at a frequency of 0.018449 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: South Asian in 1395 of 30540 chromosomes (freq: 0.04568), European (non-Finnish) in 2954 of 128924 chromosomes (freq: 0.02291), Ashkenazi Jewish in 197 of 10352 chromosomes (freq: 0.01903), Other in 114 of 7212 chromosomes (freq: 0.01581), European (Finnish) in 194 of 25090 chromosomes (freq: 0.007732), Latino in 246 of 35372 chromosomes (freq: 0.006955), African in 105 of 24924 chromosomes (freq: 0.004213) and East Asian in 4 of 19926 chromosomes (freq: 0.000201). This variant was identified in an unaffected carrier with another disease-causing mutation for Tay-Sachs disease, suggesting that this variant is not associated with disease (Triggs-Rainer_1995_PMID:7717398). The c.705+30T>G variant occurs outside the splicing consensus sequence and is not predicted to have an impact on splicing by 4 of 4 in silico splicing softwares (SpliceSiteFinder-Like, MaxEntScan, NNSplice, GeneSplicer). In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 30, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: frequency. OB 12/23/15: 4.6% freq in South Asian chr - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 11, 2019 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 9150157, 28492530, 22723944, 27535533, 27884173, 7717398) - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 05, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
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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