chr19-9854147-A-G

Position:

• chr19-9854147-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.38

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 -14 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_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.921 AC: 139983 AN: 152002 Hom.: 65064 Cov.: 30

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

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.: 29 AF XY: 0.963 AC XY: 695036 AN XY: 722036

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.: 30 AF XY: 0.918 AC XY: 68243 AN XY: 74366

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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

Other links and lift over

dbSNP: rs8111802; hg19: chr19-9964823;