rs1326497740

Variant names:

• chr1-156624123-C-A
• rs1326497740
• NM_021817.3:c.402C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-156624123-C-A
• chr1-156624123-C-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_021817.3(HAPLN2):​c.402C>A​(p.Ile134Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: HAPLN2 NM_021817.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

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]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BP7: Synonymous conserved (PhyloP=-1.9 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAPLN2	NM_021817.3	c.402C>A	p.Ile134Ile	synonymous_variant	Exon 4 of 7	ENST00000255039.6	NP_068589.1
HAPLN2	XM_011509853.3	c.402C>A	p.Ile134Ile	synonymous_variant	Exon 4 of 7		XP_011508155.1
HAPLN2	XM_017002020.2	c.402C>A	p.Ile134Ile	synonymous_variant	Exon 5 of 8		XP_016857509.1
HAPLN2	XM_047427123.1	c.535C>A	p.Arg179Arg	synonymous_variant	Exon 5 of 5		XP_047283079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAPLN2	ENST00000255039.6	c.402C>A	p.Ile134Ile	synonymous_variant	Exon 4 of 7	1	NM_021817.3	ENSP00000255039.1
HAPLN2	ENST00000456112.1	c.402C>A	p.Ile134Ile	synonymous_variant	Exon 4 of 5	5		ENSP00000388835.1
HAPLN2	ENST00000494218.1	n.60C>A		non_coding_transcript_exon_variant	Exon 1 of 3	2
HAPLN2	ENST00000482204.1	n.*209C>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	6.3
DANN	Benign	0.91

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: rs1326497740; hg19: chr1-156593915;