Variant chr19-9854270-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_058164.4(OLFM2):c.1281C>T(p.Arg427=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,613,892 control chromosomes in the GnomAD database, including 11,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.099 ( 861 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10946 hom. )

Consequence

OLFM2
NM_058164.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.771

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 19-9854270-G-A is Benign according to our data. Variant chr19-9854270-G-A is described in ClinVar as [Benign]. Clinvar id is 1238007.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.771 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
OLFM2	NM_058164.4 linkuse as main transcript	c.1281C>T	p.Arg427=	synonymous_variant	6/6	ENST00000264833.9
OLFM2	NM_001304347.2 linkuse as main transcript	c.1353C>T	p.Arg451=	synonymous_variant	6/6
OLFM2	NM_001304348.2 linkuse as main transcript	c.1047C>T	p.Arg349=	synonymous_variant	5/5
OLFM2	XM_047439713.1 linkuse as main transcript	c.1077C>T	p.Arg359=	synonymous_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
OLFM2	ENST00000264833.9 linkuse as main transcript	c.1281C>T	p.Arg427=	synonymous_variant	6/6	1	NM_058164.4
OLFM2	ENST00000593091.2 linkuse as main transcript	c.1353C>T	p.Arg451=	synonymous_variant	6/6	5		P1
OLFM2	ENST00000590841.5 linkuse as main transcript	c.1047C>T	p.Arg349=	synonymous_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.0986

AC:

14994

AN:

152012

Hom.:

863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0514

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.0856

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0964

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.111

GnomAD3 exomes

AF:

0.111

AC:

27833

AN:

251476

Hom.:

1699

AF XY:

0.118

AC XY:

16025

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.0534

Gnomad AMR exome

AF:

0.0598

Gnomad ASJ exome

AF:

0.150

Gnomad EAS exome

AF:

0.0996

Gnomad SAS exome

AF:

0.152

Gnomad FIN exome

AF:

0.0997

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.119

AC:

174403

AN:

1461762

Hom.:

10946

Cov.:

AF XY:

0.122

AC XY:

88604

AN XY:

727192

show subpopulations

Gnomad4 AFR exome

AF:

0.0519

Gnomad4 AMR exome

AF:

0.0627

Gnomad4 ASJ exome

AF:

0.151

Gnomad4 EAS exome

AF:

0.0830

Gnomad4 SAS exome

AF:

0.154

Gnomad4 FIN exome

AF:

0.0979

Gnomad4 NFE exome

AF:

0.122

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.0985

AC:

14985

AN:

152130

Hom.:

861

Cov.:

AF XY:

0.0990

AC XY:

7363

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0513

Gnomad4 AMR

AF:

0.0854

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.0963

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.102

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.116

Hom.:

603

Bravo

AF:

0.0947

Asia WGS

AF:

0.0980

AC:

338

AN:

3478

EpiCase

AF:

0.135

EpiControl

AF:

0.135

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	This variant is associated with the following publications: (PMID: 17122126) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.3

DANN

Benign

0.89

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over