1-162018416-C-T

Variant names:

• chr1-162018416-C-T
• rs7532680
• NM_015441.3:c.439-909G>A

Variant summary

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

The NM_015441.3(OLFML2B):​c.439-909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,056 control chromosomes in the GnomAD database, including 14,157 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 0.36 (14157 hom., cov: 33)
• Consequence: OLFML2B NM_015441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFML2B	NM_015441.3	MANE Select	c.439-909G>A		intron	N/A	NP_056256.1	Q68BL8-1
	OLFML2B	NM_001347700.2		c.439-909G>A		intron	N/A	NP_001334629.1
	OLFML2B	NM_001297713.2		c.439-909G>A		intron	N/A	NP_001284642.1	F2Z3N3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFML2B	ENST00000294794.8	TSL:1 MANE Select	c.439-909G>A		intron	N/A	ENSP00000294794.3	Q68BL8-1
	OLFML2B	ENST00000367940.2	TSL:2	c.439-909G>A		intron	N/A	ENSP00000356917.2	F2Z3N3

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54357 AN: 151938 Hom.: 14128 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.358 AC: 54438 AN: 152056 Hom.: 14157 Cov.: 33 AF XY: 0.357 AC XY: 26550 AN XY: 74306

African (AFR) AF: 0.735 AC: 30456 AN: 41440

American (AMR) AF: 0.235 AC: 3595 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2178 AN: 5164

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2264 AN: 10594

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12529 AN: 67986

Other (OTH) AF: 0.319 AC: 673 AN: 2108

Alfa AF: 0.244 Hom.: 7957

Bravo AF: 0.374

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		0.21
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: rs7532680; hg19: chr1-161988206;