chr19-9889646-C-G

Position:

• chr19-9889646-C-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
OLFM2	NM_058164.4	c.64-28852G>C		intron_variant		ENST00000264833.9
OLFM2	NM_001304347.2	c.135+23837G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLFM2	ENST00000264833.9	c.64-28852G>C		intron_variant		1	NM_058164.4
OLFM2	ENST00000593091.2	c.135+23837G>C		intron_variant		5		P1
OLFM2	ENST00000590410.1	n.22-28852G>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.387

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

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: rs1862471; hg19: chr19-10000322;