19-9897565-C-T

Variant names:

• chr19-9897565-C-T
• rs4239546
• NM_058164.4:c.64-36771G>A

Variant summary

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

The NM_058164.4(OLFM2):​c.64-36771G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,018 control chromosomes in the GnomAD database, including 31,503 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 0.61 (31503 hom., cov: 31)
• Consequence: OLFM2 NM_058164.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM2	NM_058164.4	c.64-36771G>A		intron_variant	Intron 1 of 5	ENST00000264833.9	NP_477512.1
OLFM2	NM_001304347.2	c.135+15918G>A		intron_variant	Intron 1 of 5		NP_001291276.1
LOC124904636	XR_007067135.1	n.120-2638C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFM2	ENST00000264833.9	c.64-36771G>A		intron_variant	Intron 1 of 5	1	NM_058164.4	ENSP00000264833.3
OLFM2	ENST00000593091.2	c.135+15918G>A		intron_variant	Intron 1 of 5	5		ENSP00000465809.2
OLFM2	ENST00000590410.1	n.22-36771G>A		intron_variant	Intron 1 of 3	2
ENSG00000295575	ENST00000731017.1	n.193-2638C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93432 AN: 151900 Hom.: 31502 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.615 AC: 93454 AN: 152018 Hom.: 31503 Cov.: 31 AF XY: 0.614 AC XY: 45621 AN XY: 74304

African (AFR) AF: 0.326 AC: 13533 AN: 41460

American (AMR) AF: 0.712 AC: 10841 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2476 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2729 AN: 5142

South Asian (SAS) AF: 0.501 AC: 2418 AN: 4822

European-Finnish (FIN) AF: 0.775 AC: 8200 AN: 10578

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 51082 AN: 67994

Other (OTH) AF: 0.611 AC: 1292 AN: 2116

Alfa AF: 0.688 Hom.: 39603

Bravo AF: 0.601

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.82
PhyloP100		-0.73
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: rs4239546; hg19: chr19-10008241;