19-9890200-C-G

Variant names:

• chr19-9890200-C-G
• rs7245579
• NM_058164.4:c.64-29406G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_058164.4(OLFM2):​c.64-29406G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,110 control chromosomes in the GnomAD database, including 11,905 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 (11905 hom., cov: 32)
• Consequence: OLFM2 NM_058164.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM2	NM_058164.4	c.64-29406G>C		intron_variant	Intron 1 of 5	ENST00000264833.9	NP_477512.1
OLFM2	NM_001304347.2	c.135+23283G>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.64-29406G>C		intron_variant	Intron 1 of 5	1	NM_058164.4	ENSP00000264833.3
OLFM2	ENST00000593091.2	c.135+23283G>C		intron_variant	Intron 1 of 5	5		ENSP00000465809.2
OLFM2	ENST00000590410.1	n.22-29406G>C		intron_variant	Intron 1 of 3	2
ENSG00000295575	ENST00000731017.1	n.99-3315C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54194 AN: 151994 Hom.: 11907 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.356 AC: 54190 AN: 152110 Hom.: 11905 Cov.: 32 AF XY: 0.356 AC XY: 26486 AN XY: 74346

African (AFR) AF: 0.102 AC: 4253 AN: 41530

American (AMR) AF: 0.515 AC: 7873 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1594 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1473 AN: 5156

South Asian (SAS) AF: 0.271 AC: 1309 AN: 4828

European-Finnish (FIN) AF: 0.438 AC: 4620 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31905 AN: 67976

Other (OTH) AF: 0.373 AC: 788 AN: 2114

Alfa AF: 0.282 Hom.: 838

Bravo AF: 0.353

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	19
DANN	Benign	0.68
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7245579; hg19: chr19-10000876;