10-113552847-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001177660.3(HABP2):​c.-10+1886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,214 control chromosomes in the GnomAD database, including 1,492 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1492 hom., cov: 33)

Consequence

HABP2
NM_001177660.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.426
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 10-113552847-G-A is Benign according to our data. Variant chr10-113552847-G-A is described in ClinVar as [Benign]. Clinvar id is 1269429.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HABP2NM_001177660.3 linkuse as main transcriptc.-10+1886G>A intron_variant NP_001171131.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HABP2ENST00000542051.5 linkuse as main transcriptc.-10+1886G>A intron_variant 2 ENSP00000443283 Q14520-2

Frequencies

GnomAD3 genomes
AF:
0.122
AC:
18499
AN:
152096
Hom.:
1494
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0346
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.117
Gnomad ASJ
AF:
0.203
Gnomad EAS
AF:
0.0212
Gnomad SAS
AF:
0.0692
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.170
Gnomad OTH
AF:
0.152
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.121
AC:
18489
AN:
152214
Hom.:
1492
Cov.:
33
AF XY:
0.121
AC XY:
9000
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.0345
Gnomad4 AMR
AF:
0.117
Gnomad4 ASJ
AF:
0.203
Gnomad4 EAS
AF:
0.0213
Gnomad4 SAS
AF:
0.0692
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.170
Gnomad4 OTH
AF:
0.151
Alfa
AF:
0.163
Hom.:
2165
Bravo
AF:
0.111
Asia WGS
AF:
0.0580
AC:
202
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJan 10, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
1.4
DANN
Benign
0.72

Splicing

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.

Other links and lift over

dbSNP: rs2240880; hg19: chr10-115312606; API