rs11629508

Positions:

• chr15-72343488-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000520.6(HEXA):​c.*589T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 153,542 control chromosomes in the GnomAD database, including 48,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.74 (48303 hom., cov: 31)
  • Exomes 𝑓: 0.90 (629 hom.)
• Consequence: HEXA NM_000520.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.103

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 15-72343488-A-C is Benign according to our data. Variant chr15-72343488-A-C is described in ClinVar as [Benign]. Clinvar id is 317033.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HEXA	NM_000520.6	c.*589T>G		3_prime_UTR_variant	14/14	ENST00000268097.10	NP_000511.2
HEXA	NM_001318825.2	c.*589T>G		3_prime_UTR_variant	14/14		NP_001305754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HEXA	ENST00000268097.10	c.*589T>G		3_prime_UTR_variant	14/14	1	NM_000520.6	ENSP00000268097	P1
	ENST00000570175.1	n.166-1898A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113225 AN: 151896 Hom.: 48319 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.904 AC: 1382 AN: 1528 Hom.: 629 Cov.: 0 AF XY: 0.912 AC XY: 739 AN XY: 810

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.816

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.903

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.944

Gnomad4 OTH exome AF: 0.871

GnomAD4 genome AF: 0.745 AC: 113216 AN: 152014 Hom.: 48303 Cov.: 31 AF XY: 0.750 AC XY: 55705 AN XY: 74300

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.783

Alfa AF: 0.907 Hom.: 67850

Bravo AF: 0.719

Asia WGS AF: 0.795 AC: 2766 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Tay-Sachs disease Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11629508; hg19: chr15-72635829;