chr9-130357981-A-G

Variant names:

• chr9-130357981-A-G
• rs1840140760
• NM_001291815.2:c.5573A>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001291815.2(HMCN2):​c.5573A>G​(p.Asn1858Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000868 in 1,151,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 8.7e-7 (0 hom.)
• Consequence: HMCN2 NM_001291815.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.926
• Publications: 0 publications found

Genes affected

HMCN2 (HGNC:21293): (hemicentin 2) Predicted to enable calcium ion binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Located in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.082166314).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001291815.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMCN2	NM_001291815.2	MANE Select	c.5573A>G	p.Asn1858Ser	missense	Exon 35 of 98	NP_001278744.1	Q8NDA2-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMCN2	ENST00000683500.2	MANE Select	c.5573A>G	p.Asn1858Ser	missense	Exon 35 of 98	ENSP00000508292.2	Q8NDA2-5
	HMCN2	ENST00000624552.4	TSL:5	c.5573A>G	p.Asn1858Ser	missense	Exon 35 of 98	ENSP00000485357.2	Q8NDA2-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.68e-7 AC: 1 AN: 1151604 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 564670

African (AFR) AF: 0.00 AC: 0 AN: 24412

American (AMR) AF: 0.00 AC: 0 AN: 28242

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15890

East Asian (EAS) AF: 0.00 AC: 0 AN: 12838

South Asian (SAS) AF: 0.00 AC: 0 AN: 76182

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27290

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4400

European-Non Finnish (NFE) AF: 0.00000109 AC: 1 AN: 920748

Other (OTH) AF: 0.00 AC: 0 AN: 41602

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.40	T
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.20
DANN	Benign	0.37
DEOGEN2	Benign	0.00093	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0092	N
LIST_S2	Benign	0.39	T
MetaRNN	Benign	0.082	T
PhyloP100		-0.93
Sift4G	Benign	0.62	T
Vest4		0.050
MVP		0.030
ClinPred		0.047	T
GERP RS		-9.5
Varity_R		0.038
gMVP		0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1840140760; hg19: chr9-133233368;