Genetic Variant OLFM1:p.Cys152HisfsTer19 (chr9-135077150-G-GCA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000371799.8(OLFM1):c.452_453dupCA(p.Cys152HisfsTer19) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0258 in 1,507,044 control chromosomes in the GnomAD database, including 984 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 599 hom., cov: 32)

Exomes 𝑓: 0.022 ( 385 hom. )

Consequence

OLFM1
ENST00000371799.8 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.399

Publications

4 publications found

Variant links:

Genes affected

OLFM1 (HGNC:17187): (olfactomedin 1) This gene product shares extensive sequence similarity with the rat neuronal olfactomedin-related ER localized protein. While the exact function of the encoded protein is not known, its abundant expression in brain suggests that it may have an essential role in nerve tissue. Several alternatively spliced transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

OLFM1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371799.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM1	NM_014279.7		c.66+1365_66+1366dupCA		intron	N/A	NP_055094.2
	OLFM1	NM_006334.6		c.66+1365_66+1366dupCA		intron	N/A	NP_006325.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OLFM1	ENST00000371799.8	TSL:1	c.452_453dupCA	p.Cys152HisfsTer19	frameshift	Exon 2 of 2	ENSP00000360864.4	Q6IMJ6
OLFM1	ENST00000252854.8	TSL:1	c.96+1365_96+1366dupCA		intron	N/A	ENSP00000252854.4	Q99784-3
OLFM1	ENST00000277415.15	TSL:1	c.96+1365_96+1366dupCA		intron	N/A	ENSP00000277415.11	Q99784-4

Frequencies

GnomAD3 genomes

AF:

0.0629

AC:

9504

AN:

151138

Hom.:

597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0346

Gnomad ASJ

AF:

0.0229

Gnomad EAS

AF:

0.00175

Gnomad SAS

AF:

0.0111

Gnomad FIN

AF:

0.0526

Gnomad MID

AF:

0.0290

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.0541

GnomAD2 exomes

AF:

0.0332

AC:

3659

AN:

110262

AF XY:

0.0303

show subpopulations

Gnomad AFR exome

AF:

0.165

Gnomad AMR exome

AF:

0.0283

Gnomad ASJ exome

AF:

0.0348

Gnomad EAS exome

AF:

0.00231

Gnomad FIN exome

AF:

0.0558

Gnomad NFE exome

AF:

0.0237

Gnomad OTH exome

AF:

0.0385

GnomAD4 exome

AF:

0.0216

AC:

29321

AN:

1355800

Hom.:

385

Cov.:

AF XY:

0.0207

AC XY:

13844

AN XY:

667994

show subpopulations

African (AFR)

AF:

0.168

AC:

5171

AN:

30692

American (AMR)

AF:

0.0252

AC:

867

AN:

34442

Ashkenazi Jewish (ASJ)

AF:

0.0236

AC:

567

AN:

24062

East Asian (EAS)

AF:

0.00673

AC:

228

AN:

33884

South Asian (SAS)

AF:

0.00896

AC:

679

AN:

75780

European-Finnish (FIN)

AF:

0.0341

AC:

1580

AN:

46296

Middle Eastern (MID)

AF:

0.0354

AC:

196

AN:

5536

European-Non Finnish (NFE)

AF:

0.0176

AC:

18488

AN:

1049064

Other (OTH)

AF:

0.0276

AC:

1545

AN:

56044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

1782

3565

5347

7130

8912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

800

1600

2400

3200

4000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0630

AC:

9521

AN:

151244

Hom.:

599

Cov.:

AF XY:

0.0632

AC XY:

4668

AN XY:

73884

show subpopulations

African (AFR)

AF:

0.170

AC:

7026

AN:

41220

American (AMR)

AF:

0.0346

AC:

526

AN:

15204

Ashkenazi Jewish (ASJ)

AF:

0.0229

AC:

AN:

3456

East Asian (EAS)

AF:

0.00175

AC:

AN:

5140

South Asian (SAS)

AF:

0.0109

AC:

AN:

4770

European-Finnish (FIN)

AF:

0.0526

AC:

550

AN:

10448

Middle Eastern (MID)

AF:

0.0280

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.0171

AC:

1159

AN:

67718

Other (OTH)

AF:

0.0535

AC:

112

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

405

810

1215

1620

2025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0130

Hom.:

Bravo

AF:

0.0663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.40

Mutation Taster

=184/16

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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9-135077150-GCACACACACA-GCACACACACACA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over