rs1862471

Variant names:

• chr19-9889646-C-G
• rs1862471
• NM_058164.4:c.64-28852G>C

Variant summary

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

The NM_058164.4(OLFM2):​c.64-28852G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,138 control chromosomes in the GnomAD database, including 12,523 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 0.38 (12523 hom., cov: 32)
• Consequence: OLFM2 NM_058164.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 13 publications found

Genes affected

OLFM2 (HGNC:17189): (olfactomedin 2) Involved in positive regulation of smooth muscle cell differentiation. Acts upstream of or within protein secretion. Located in cytoplasm; extracellular region; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000295575 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM2	NM_058164.4	c.64-28852G>C		intron_variant	Intron 1 of 5	ENST00000264833.9	NP_477512.1
OLFM2	NM_001304347.2	c.135+23837G>C		intron_variant	Intron 1 of 5		NP_001291276.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFM2	ENST00000264833.9	c.64-28852G>C		intron_variant	Intron 1 of 5	1	NM_058164.4	ENSP00000264833.3
OLFM2	ENST00000593091.2	c.135+23837G>C		intron_variant	Intron 1 of 5	5		ENSP00000465809.2
OLFM2	ENST00000590410.1	n.22-28852G>C		intron_variant	Intron 1 of 3	2
ENSG00000295575	ENST00000731017.1	n.99-3869C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58062 AN: 152020 Hom.: 12524 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.382 AC: 58068 AN: 152138 Hom.: 12523 Cov.: 32 AF XY: 0.381 AC XY: 28363 AN XY: 74364

African (AFR) AF: 0.191 AC: 7916 AN: 41536

American (AMR) AF: 0.522 AC: 7979 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1467 AN: 5156

South Asian (SAS) AF: 0.270 AC: 1299 AN: 4816

European-Finnish (FIN) AF: 0.440 AC: 4656 AN: 10586

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31972 AN: 67994

Other (OTH) AF: 0.387 AC: 815 AN: 2106

Alfa AF: 0.426 Hom.: 1825

Bravo AF: 0.382

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.63
PhyloP100		-1.1
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: rs1862471; hg19: chr19-10000322;