19-9855016-T-C

Position:

• chr19-9855016-T-C

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.688-153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,074 control chromosomes in the GnomAD database, including 2,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2890 hom., cov: 31)
• Consequence: OLFM2 NM_058164.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.17

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=-0.9).
• BP6: Variant 19-9855016-T-C is Benign according to our data. Variant chr19-9855016-T-C is described in ClinVar as [Benign]. Clinvar id is 1286103.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OLFM2	NM_058164.4	c.688-153A>G		intron_variant		ENST00000264833.9
OLFM2	NM_001304347.2	c.760-153A>G		intron_variant
OLFM2	NM_001304348.2	c.454-153A>G		intron_variant
OLFM2	XM_047439713.1	c.484-153A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLFM2	ENST00000264833.9	c.688-153A>G		intron_variant		1	NM_058164.4
OLFM2	ENST00000590841.5	c.454-153A>G		intron_variant		2
OLFM2	ENST00000593091.2	c.760-153A>G		intron_variant		5		P1
OLFM2	ENST00000592448.1	c.*93-153A>G		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27545 AN: 151956 Hom.: 2891 Cov.: 31

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27548 AN: 152074 Hom.: 2890 Cov.: 31 AF XY: 0.183 AC XY: 13583 AN XY: 74306

Gnomad4 AFR AF: 0.0864

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.165

Alfa AF: 0.176 Hom.: 385

Bravo AF: 0.168

Asia WGS AF: 0.215 AC: 750 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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.74

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: rs16996141; hg19: chr19-9965692;