rs932650

Variant names:

• chr10-113587600-T-C
• rs932650
• NM_004132.5:c.1519-605T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-113587600-T-C
• chr10-113587600-T-G

Variant summary

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

The NM_004132.5(HABP2):​c.1519-605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,020 control chromosomes in the GnomAD database, including 10,144 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 0.36 (10144 hom., cov: 32)
• Consequence: HABP2 NM_004132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 18 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HABP2	NM_004132.5	c.1519-605T>C		intron_variant	Intron 12 of 12	ENST00000351270.4	NP_004123.1
HABP2	NM_001177660.3	c.1441-605T>C		intron_variant	Intron 12 of 12		NP_001171131.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HABP2	ENST00000351270.4	c.1519-605T>C		intron_variant	Intron 12 of 12	1	NM_004132.5	ENSP00000277903.4
HABP2	ENST00000542051.5	c.1441-605T>C		intron_variant	Intron 12 of 12	2		ENSP00000443283.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54868 AN: 151902 Hom.: 10128 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.361 AC: 54927 AN: 152020 Hom.: 10144 Cov.: 32 AF XY: 0.359 AC XY: 26702 AN XY: 74306

African (AFR) AF: 0.382 AC: 15841 AN: 41448

American (AMR) AF: 0.460 AC: 7026 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3462

East Asian (EAS) AF: 0.318 AC: 1646 AN: 5174

South Asian (SAS) AF: 0.316 AC: 1519 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3110 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23316 AN: 67956

Other (OTH) AF: 0.355 AC: 751 AN: 2114

Alfa AF: 0.350 Hom.: 24878

Bravo AF: 0.373

Asia WGS AF: 0.323 AC: 1121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.28
PhyloP100		-0.54
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: rs932650; hg19: chr10-115347359;