Variant chr10-113553052-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001177660.3(HABP2):c.-10+2091T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,067,296 control chromosomes in the GnomAD database, including 65,312 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8406 hom., cov: 33)

Exomes 𝑓: 0.34 ( 56906 hom. )

Consequence

HABP2
NM_001177660.3 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.84

Variant links:

Genes affected

HABP2 (HGNC:4798): (hyaluronan binding protein 2) This gene encodes a member of the peptidase S1 family of serine proteases. The encoded preproprotein is secreted by hepatocytes and proteolytically processed to generate heavy and light chains that form the mature heterodimer. Further autoproteolysis leads to smaller, inactive peptides. This extracellular protease binds hyaluronic acid and may play a role in the coagulation and fibrinolysis systems. Mutations in this gene are associated with nonmedullary thyroid cancer and susceptibility to venous thromboembolism. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

HABP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 10-113553052-T-C is Benign according to our data. Variant chr10-113553052-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 298892.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HABP2	NM_001177660.3 linkuse as main transcript	c.-10+2091T>C		intron_variant
HABP2	NM_004132.5 linkuse as main transcript			upstream_gene_variant		ENST00000351270.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HABP2	ENST00000542051.5 linkuse as main transcript	c.-10+2091T>C		intron_variant		2			Q14520-2
HABP2	ENST00000351270.4 linkuse as main transcript			upstream_gene_variant		1	NM_004132.5	P1	Q14520-1

Frequencies

GnomAD3 genomes

AF:

0.330

AC:

50035

AN:

151808

Hom.:

8401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.375

GnomAD4 exome

AF:

0.343

AC:

314105

AN:

915368

Hom.:

56906

Cov.:

AF XY:

0.351

AC XY:

166516

AN XY:

474072

show subpopulations

Gnomad4 AFR exome

AF:

0.308

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.407

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.474

Gnomad4 FIN exome

AF:

0.323

Gnomad4 NFE exome

AF:

0.342

Gnomad4 OTH exome

AF:

0.355

GnomAD4 genome

AF:

0.330

AC:

50064

AN:

151928

Hom.:

8406

Cov.:

AF XY:

0.331

AC XY:

24575

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.408

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.466

Gnomad4 FIN

AF:

0.319

Gnomad4 NFE

AF:

0.346

Gnomad4 OTH

AF:

0.371

Alfa

AF:

0.341

Hom.:

4534

Bravo

AF:

0.319

Asia WGS

AF:

0.317

AC:

1103

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	- -

Factor VII Marburg I Variant Thrombophilia

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

6.7

DANN

Benign

0.80

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