19-9897565-C-T

Position:

• chr19-9897565-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

OLFM2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
OLFM2	NM_058164.4	c.64-36771G>A		intron_variant		ENST00000264833.9	NP_477512.1
OLFM2	NM_001304347.2	c.135+15918G>A		intron_variant			NP_001291276.1
LOC124904636	XR_007067135.1	n.120-2638C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFM2	ENST00000264833.9	c.64-36771G>A		intron_variant		1	NM_058164.4	ENSP00000264833.3
OLFM2	ENST00000593091.2	c.135+15918G>A		intron_variant		5		ENSP00000465809.2
OLFM2	ENST00000590410.1	n.22-36771G>A		intron_variant		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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.611

Alfa AF: 0.698 Hom.: 29280

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

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: rs4239546; hg19: chr19-10008241;