1-162006444-A-G

Variant names:

• chr1-162006444-A-G
• rs12022536
• NM_015441.3:c.576T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_015441.3(OLFML2B):​c.576T>C​(p.Asn192Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 1,596,428 control chromosomes in the GnomAD database, including 494,574 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 0.71 (39771 hom., cov: 26)
  • Exomes 𝑓: 0.79 (454803 hom.)
• Consequence: OLFML2B NM_015441.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 20 publications found

Genes affected

OLFML2B (HGNC:24558): (olfactomedin like 2B) This gene encodes an olfactomedin domain-containing protein. Most olfactomedin domain-containing proteins are secreted glycoproteins. [provided by RefSeq, Dec 2016]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP7: Synonymous conserved (PhyloP=-1.75 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015441.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFML2B	NM_015441.3	MANE Select	c.576T>C	p.Asn192Asn	synonymous	Exon 4 of 8	NP_056256.1
	OLFML2B	NM_001347700.2		c.576T>C	p.Asn192Asn	synonymous	Exon 4 of 8	NP_001334629.1
	OLFML2B	NM_001297713.2		c.576T>C	p.Asn192Asn	synonymous	Exon 4 of 8	NP_001284642.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFML2B	ENST00000294794.8	TSL:1 MANE Select	c.576T>C	p.Asn192Asn	synonymous	Exon 4 of 8	ENSP00000294794.3
	OLFML2B	ENST00000367940.2	TSL:2	c.576T>C	p.Asn192Asn	synonymous	Exon 4 of 8	ENSP00000356917.2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 107125 AN: 150232 Hom.: 39759 Cov.: 26

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.729

GnomAD2 exomes AF: 0.741 AC: 175505 AN: 237002 AF XY: 0.739

Gnomad AFR exome AF: 0.500

Gnomad AMR exome AF: 0.805

Gnomad ASJ exome AF: 0.768

Gnomad EAS exome AF: 0.474

Gnomad FIN exome AF: 0.816

Gnomad NFE exome AF: 0.821

Gnomad OTH exome AF: 0.774

GnomAD4 exome AF: 0.788 AC: 1138992 AN: 1446078 Hom.: 454803 Cov.: 42 AF XY: 0.782 AC XY: 562938 AN XY: 719638

African (AFR) AF: 0.487 AC: 15677 AN: 32194

American (AMR) AF: 0.801 AC: 32638 AN: 40742

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 19701 AN: 25528

East Asian (EAS) AF: 0.515 AC: 20184 AN: 39224

South Asian (SAS) AF: 0.579 AC: 48312 AN: 83496

European-Finnish (FIN) AF: 0.822 AC: 43065 AN: 52394

Middle Eastern (MID) AF: 0.718 AC: 4079 AN: 5680

European-Non Finnish (NFE) AF: 0.822 AC: 910276 AN: 1107184

Other (OTH) AF: 0.756 AC: 45060 AN: 59636

GnomAD4 genome AF: 0.713 AC: 107173 AN: 150350 Hom.: 39771 Cov.: 26 AF XY: 0.712 AC XY: 52137 AN XY: 73224

African (AFR) AF: 0.508 AC: 20683 AN: 40720

American (AMR) AF: 0.794 AC: 12021 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2653 AN: 3460

East Asian (EAS) AF: 0.481 AC: 2435 AN: 5060

South Asian (SAS) AF: 0.588 AC: 2749 AN: 4672

European-Finnish (FIN) AF: 0.815 AC: 8299 AN: 10178

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.822 AC: 55788 AN: 67848

Other (OTH) AF: 0.727 AC: 1504 AN: 2070

Alfa AF: 0.781 Hom.: 164042

Bravo AF: 0.702

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.34
DANN	Benign	0.39
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12022536; hg19: chr1-161976234; COSMIC: COSV108110064;