1-162018416-C-T

Position:

• chr1-162018416-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFML2B	NM_015441.3	c.439-909G>A		intron_variant		ENST00000294794.8	NP_056256.1
OLFML2B	NM_001347700.2	c.439-909G>A		intron_variant			NP_001334629.1
OLFML2B	NM_001297713.2	c.439-909G>A		intron_variant			NP_001284642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFML2B	ENST00000294794.8	c.439-909G>A		intron_variant		1	NM_015441.3	ENSP00000294794.3
OLFML2B	ENST00000367940.2	c.439-909G>A		intron_variant		2		ENSP00000356917.2

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

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.319

Alfa AF: 0.225 Hom.: 4957

Bravo AF: 0.374

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.59

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: rs7532680; hg19: chr1-161988206;