Variant 17-82419814-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001330542.2(HEXD):c.15T>G(p.Thr5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,601,768 control chromosomes in the GnomAD database, including 94,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 14706 hom., cov: 32)

Exomes 𝑓: 0.32 ( 79455 hom. )

Consequence

HEXD
NM_001330542.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.20

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 17-82419814-T-G is Benign according to our data. Variant chr17-82419814-T-G is described in ClinVar as [Benign]. Clinvar id is 402932.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HEXD	NM_001330542.2 linkuse as main transcript	c.15T>G	p.Thr5=	synonymous_variant	2/13	ENST00000327949.15	NP_001317471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HEXD	ENST00000327949.15 linkuse as main transcript	c.15T>G	p.Thr5=	synonymous_variant	2/13	1	NM_001330542.2	ENSP00000332634	P1	Q8WVB3-1

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62173

AN:

151956

Hom.:

14663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.708

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.414

GnomAD3 exomes

AF:

0.356

AC:

88312

AN:

248414

Hom.:

17847

AF XY:

0.341

AC XY:

45987

AN XY:

134918

show subpopulations

Gnomad AFR exome

AF:

0.635

Gnomad AMR exome

AF:

0.420

Gnomad ASJ exome

AF:

0.299

Gnomad EAS exome

AF:

0.700

Gnomad SAS exome

AF:

0.266

Gnomad FIN exome

AF:

0.250

Gnomad NFE exome

AF:

0.294

Gnomad OTH exome

AF:

0.329

GnomAD4 exome

AF:

0.317

AC:

460111

AN:

1449692

Hom.:

79455

Cov.:

AF XY:

0.314

AC XY:

226351

AN XY:

721826

show subpopulations

Gnomad4 AFR exome

AF:

0.632

Gnomad4 AMR exome

AF:

0.415

Gnomad4 ASJ exome

AF:

0.299

Gnomad4 EAS exome

AF:

0.713

Gnomad4 SAS exome

AF:

0.267

Gnomad4 FIN exome

AF:

0.254

Gnomad4 NFE exome

AF:

0.296

Gnomad4 OTH exome

AF:

0.340

GnomAD4 genome

AF:

0.409

AC:

62265

AN:

152076

Hom.:

14706

Cov.:

AF XY:

0.404

AC XY:

30063

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.623

Gnomad4 AMR

AF:

0.395

Gnomad4 ASJ

AF:

0.304

Gnomad4 EAS

AF:

0.708

Gnomad4 SAS

AF:

0.269

Gnomad4 FIN

AF:

0.247

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.415

Alfa

AF:

0.308

Hom.:

7857

Bravo

AF:

0.434

Asia WGS

AF:

0.465

AC:

1615

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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 -

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

-0.92

CADD

Benign

0.099

DANN

Benign

0.63

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