rs4918851

chr10-113565686-C-Achr10-113565686-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004132.5(HABP2):c.70-1803C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,100 control chromosomes in the GnomAD database, including 9,403 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (9403 hom., cov: 33)
• Consequence: HABP2 NM_004132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HABP2	NM_004132.5	c.70-1803C>A		intron_variant		ENST00000351270.4
HABP2	NM_001177660.3	c.-9-1803C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HABP2	ENST00000351270.4	c.70-1803C>A		intron_variant		1	NM_004132.5	P1
HABP2	ENST00000542051.5	c.-9-1803C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49491 AN: 151980 Hom.: 9375 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.326 AC: 49570 AN: 152100 Hom.: 9403 Cov.: 33 AF XY: 0.326 AC XY: 24222 AN XY: 74372

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.327

Alfa AF: 0.251 Hom.: 2681

Bravo AF: 0.361

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.3
Dann	Benign	0.73

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: rs4918851; hg19: chr10-115325445;