Variant chr19-9854147-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_058164.4(OLFM2):c.*39T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 1,602,956 control chromosomes in the GnomAD database, including 744,491 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.92 ( 65083 hom., cov: 30)

Exomes 𝑓: 0.96 ( 679408 hom. )

Consequence

OLFM2
NM_058164.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.38

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 19-9854147-A-G is Benign according to our data. Variant chr19-9854147-A-G is described in ClinVar as [Benign]. Clinvar id is 1244938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
OLFM2	NM_058164.4 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	6/6	ENST00000264833.9
OLFM2	NM_001304347.2 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	6/6
OLFM2	NM_001304348.2 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	5/5
OLFM2	XM_047439713.1 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
OLFM2	ENST00000264833.9 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	6/6	1	NM_058164.4
OLFM2	ENST00000590841.5 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	5/5	2
OLFM2	ENST00000593091.2 linkuse as main transcript	c.*39T>C	3_prime_UTR_variant	6/6	5		P1

Frequencies

GnomAD3 genomes

AF:

0.921

AC:

139983

AN:

152002

Hom.:

65064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.826

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.910

Gnomad ASJ

AF:

0.982

Gnomad EAS

AF:

0.660

Gnomad SAS

AF:

0.835

Gnomad FIN

AF:

0.987

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.992

Gnomad OTH

AF:

0.917

GnomAD3 exomes

AF:

0.921

AC:

226806

AN:

246272

Hom.:

105592

AF XY:

0.924

AC XY:

123406

AN XY:

133608

show subpopulations

Gnomad AFR exome

AF:

0.826

Gnomad AMR exome

AF:

0.875

Gnomad ASJ exome

AF:

0.979

Gnomad EAS exome

AF:

0.667

Gnomad SAS exome

AF:

0.843

Gnomad FIN exome

AF:

0.989

Gnomad NFE exome

AF:

0.992

Gnomad OTH exome

AF:

0.949

GnomAD4 exome

AF:

0.965

AC:

1399982

AN:

1450836

Hom.:

679408

Cov.:

AF XY:

0.963

AC XY:

695036

AN XY:

722036

show subpopulations

Gnomad4 AFR exome

AF:

0.822

Gnomad4 AMR exome

AF:

0.875

Gnomad4 ASJ exome

AF:

0.978

Gnomad4 EAS exome

AF:

0.651

Gnomad4 SAS exome

AF:

0.846

Gnomad4 FIN exome

AF:

0.989

Gnomad4 NFE exome

AF:

0.993

Gnomad4 OTH exome

AF:

0.945

GnomAD4 genome

AF:

0.921

AC:

140051

AN:

152120

Hom.:

65083

Cov.:

AF XY:

0.918

AC XY:

68243

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.826

Gnomad4 AMR

AF:

0.909

Gnomad4 ASJ

AF:

0.982

Gnomad4 EAS

AF:

0.660

Gnomad4 SAS

AF:

0.836

Gnomad4 FIN

AF:

0.987

Gnomad4 NFE

AF:

0.992

Gnomad4 OTH

AF:

0.911

Alfa

AF:

0.965

Hom.:

16290

Bravo

AF:

0.910

Asia WGS

AF:

0.752

AC:

2619

AN:

3478

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.13

DANN

Benign

0.56

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