rs10986432

chr9-124808361-T-Cchr9-124808361-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182487.4(OLFML2A):c.1354+395T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,164 control chromosomes in the GnomAD database, including 2,413 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 0.16 (2413 hom., cov: 32)
• Consequence: OLFML2A NM_182487.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

Genes affected

OLFML2A (HGNC:27270): (olfactomedin like 2A) Predicted to enable extracellular matrix binding activity and identical protein binding activity. Predicted to act upstream of or within extracellular matrix organization. Predicted to be located in extracellular matrix and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OLFML2A	NM_182487.4	c.1354+395T>C		intron_variant		ENST00000373580.8
OLFML2A	NM_001282715.2	c.712+395T>C		intron_variant
OLFML2A	XM_005251760.6	c.1105+395T>C		intron_variant
OLFML2A	XM_006716989.3	c.1246+395T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLFML2A	ENST00000373580.8	c.1354+395T>C		intron_variant		1	NM_182487.4	P2
OLFML2A	ENST00000288815.5	c.712+395T>C		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24963 AN: 152046 Hom.: 2404 Cov.: 32

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.164 AC: 24975 AN: 152164 Hom.: 2413 Cov.: 32 AF XY: 0.168 AC XY: 12506 AN XY: 74406

Gnomad4 AFR AF: 0.0686

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.174

Alfa AF: 0.181 Hom.: 5085

Bravo AF: 0.166

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	11
Dann	Benign	0.84

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: rs10986432; hg19: chr9-127570640;