Variant chr1-156619658-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021817.3(HAPLN2):c.-166+123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,924 control chromosomes in the GnomAD database, including 4,856 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 0.25 ( 4851 hom., cov: 30)

Exomes 𝑓: 0.35 ( 5 hom. )

Consequence

HAPLN2
NM_021817.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Variant links:

Genes affected

HAPLN2 (HGNC:17410): (hyaluronan and proteoglycan link protein 2) Predicted to enable hyaluronic acid binding activity. Predicted to be involved in central nervous system development and skeletal system development. Predicted to act upstream of or within establishment of blood-nerve barrier and extracellular matrix assembly. Predicted to be located in extracellular region. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

HAPLN2 links:

LOC101928177 (HGNC:):

LOC101928177 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HAPLN2	NM_021817.3 link	c.-166+123C>T		intron_variant		ENST00000255039.6	NP_068589.1	Q9GZV7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
HAPLN2	ENST00000255039.6 link	c.-166+123C>T	intron_variant	1	NM_021817.3	ENSP00000255039.1	Q9GZV7
HAPLN2	ENST00000456112.1 link	c.-215+123C>T	intron_variant	5		ENSP00000388835.1	Q5T3J1
HAPLN2	ENST00000482204.1 link	n.90+123C>T	intron_variant	2
HAPLN2	ENST00000487988.5 link	n.205+123C>T	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37428

AN:

151744

Hom.:

4837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.265

GnomAD4 exome

AF:

0.350

AC:

AN:

Hom.:

AF XY:

0.357

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.375

Gnomad4 NFE exome

AF:

0.326

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.247

AC:

37476

AN:

151864

Hom.:

4851

Cov.:

AF XY:

0.250

AC XY:

18591

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.277

Gnomad4 EAS

AF:

0.363

Gnomad4 SAS

AF:

0.489

Gnomad4 FIN

AF:

0.213

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.258

Hom.:

2505

Bravo

AF:

0.243

Asia WGS

AF:

0.451

AC:

1569

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

9.6

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over