Variant 17-82436654-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001330542.2(HEXD):c.632-13G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 1,600,844 control chromosomes in the GnomAD database, including 105,334 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 10895 hom., cov: 34)

Exomes 𝑓: 0.34 ( 94439 hom. )

Consequence

HEXD
NM_001330542.2 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.674

Variant links:

Genes affected

HEXD (HGNC:26307): (hexosaminidase D) Enables beta-N-acetylhexosaminidase activity. Predicted to be involved in carbohydrate metabolic process. Located in extracellular vesicle. [provided by Alliance of Genome Resources, Apr 2022]

HEXD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 17-82436654-G-T is Benign according to our data. Variant chr17-82436654-G-T is described in ClinVar as [Benign]. Clinvar id is 402934.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HEXD	NM_001330542.2 linkuse as main transcript	c.632-13G>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000327949.15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HEXD	ENST00000327949.15 linkuse as main transcript	c.632-13G>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001330542.2	P1	Q8WVB3-1

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54405

AN:

152086

Hom.:

10883

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.451

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.359

Gnomad EAS

AF:

0.906

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.389

GnomAD3 exomes

AF:

0.417

AC:

96254

AN:

230950

Hom.:

23806

AF XY:

0.405

AC XY:

50958

AN XY:

125916

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.614

Gnomad ASJ exome

AF:

0.360

Gnomad EAS exome

AF:

0.914

Gnomad SAS exome

AF:

0.410

Gnomad FIN exome

AF:

0.285

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.391

GnomAD4 exome

AF:

0.341

AC:

494649

AN:

1448640

Hom.:

94439

Cov.:

AF XY:

0.342

AC XY:

246115

AN XY:

720220

show subpopulations

Gnomad4 AFR exome

AF:

0.332

Gnomad4 AMR exome

AF:

0.598

Gnomad4 ASJ exome

AF:

0.359

Gnomad4 EAS exome

AF:

0.913

Gnomad4 SAS exome

AF:

0.407

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.307

Gnomad4 OTH exome

AF:

0.364

GnomAD4 genome

AF:

0.358

AC:

54444

AN:

152204

Hom.:

10895

Cov.:

AF XY:

0.363

AC XY:

27013

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.325

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.359

Gnomad4 EAS

AF:

0.906

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.288

Gnomad4 NFE

AF:

0.308

Gnomad4 OTH

AF:

0.393

Alfa

AF:

0.300

Hom.:

2500

Bravo

AF:

0.380

Asia WGS

AF:

0.629

AC:

2185

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

Cadd

Benign

0.018

Dann

Benign

0.44

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over