chr10-113570889-T-C

Variant names:

• chr10-113570889-T-C
• rs6585234
• NM_004132.5:c.106+3364T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004132.5(HABP2):​c.106+3364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,092 control chromosomes in the GnomAD database, including 43,888 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 0.75 (43888 hom., cov: 32)
• Consequence: HABP2 NM_004132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004132.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HABP2	NM_004132.5	MANE Select	c.106+3364T>C		intron	N/A	NP_004123.1
	HABP2	NM_001177660.3		c.28+3364T>C		intron	N/A	NP_001171131.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HABP2	ENST00000351270.4	TSL:1 MANE Select	c.106+3364T>C		intron	N/A	ENSP00000277903.4
	HABP2	ENST00000542051.5	TSL:2	c.28+3364T>C		intron	N/A	ENSP00000443283.1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113786 AN: 151974 Hom.: 43857 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.749 AC: 113868 AN: 152092 Hom.: 43888 Cov.: 32 AF XY: 0.749 AC XY: 55670 AN XY: 74338

African (AFR) AF: 0.548 AC: 22715 AN: 41466

American (AMR) AF: 0.831 AC: 12721 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2755 AN: 3472

East Asian (EAS) AF: 0.941 AC: 4864 AN: 5168

South Asian (SAS) AF: 0.818 AC: 3941 AN: 4818

European-Finnish (FIN) AF: 0.771 AC: 8156 AN: 10572

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56158 AN: 67980

Other (OTH) AF: 0.778 AC: 1642 AN: 2110

Alfa AF: 0.750 Hom.: 6053

Bravo AF: 0.748

Asia WGS AF: 0.848 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.86
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6585234; hg19: chr10-115330648;