1-162014745-T-C

Variant names:

• chr1-162014745-T-C
• rs12026931
• NM_015441.3:c.546+2655A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015441.3(OLFML2B):​c.546+2655A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 152,300 control chromosomes in the GnomAD database, including 609 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 0.080 (609 hom., cov: 32)
• Consequence: OLFML2B NM_015441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFML2B	NM_015441.3	c.546+2655A>G		intron_variant	Intron 3 of 7	ENST00000294794.8	NP_056256.1
OLFML2B	NM_001347700.2	c.546+2655A>G		intron_variant	Intron 3 of 7		NP_001334629.1
OLFML2B	NM_001297713.2	c.546+2655A>G		intron_variant	Intron 3 of 7		NP_001284642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFML2B	ENST00000294794.8	c.546+2655A>G		intron_variant	Intron 3 of 7	1	NM_015441.3	ENSP00000294794.3
OLFML2B	ENST00000367940.2	c.546+2655A>G		intron_variant	Intron 3 of 7	2		ENSP00000356917.2

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12194 AN: 152182 Hom.: 609 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0684

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0802 AC: 12211 AN: 152300 Hom.: 609 Cov.: 32 AF XY: 0.0798 AC XY: 5941 AN XY: 74482

African (AFR) AF: 0.0333 AC: 1384 AN: 41578

American (AMR) AF: 0.0732 AC: 1119 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3472

East Asian (EAS) AF: 0.170 AC: 882 AN: 5186

South Asian (SAS) AF: 0.159 AC: 768 AN: 4826

European-Finnish (FIN) AF: 0.0684 AC: 726 AN: 10620

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6662 AN: 68006

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.0799 Hom.: 61

Bravo AF: 0.0768

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		-0.15
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: rs12026931; hg19: chr1-161984535;