rs1885436

chr10-113577779-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004132.5(HABP2):c.449-247C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,196 control chromosomes in the GnomAD database, including 51,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.82 (51162 hom., cov: 33)
• Consequence: HABP2 NM_004132.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.272

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 10-113577779-C-G is Benign according to our data. Variant chr10-113577779-C-G is described in ClinVar as [Benign]. Clinvar id is 1288592.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HABP2	NM_004132.5	c.449-247C>G		intron_variant		ENST00000351270.4
HABP2	NM_001177660.3	c.371-247C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HABP2	ENST00000351270.4	c.449-247C>G		intron_variant		1	NM_004132.5	P1
HABP2	ENST00000542051.5	c.371-247C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124553 AN: 152078 Hom.: 51105 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.837

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.819 AC: 124672 AN: 152196 Hom.: 51162 Cov.: 33 AF XY: 0.817 AC XY: 60797 AN XY: 74406

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.838

Alfa AF: 0.812 Hom.: 6211

Bravo AF: 0.828

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.61

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: rs1885436; hg19: chr10-115337538;