Genetic Variant OLFM1:c.783+105A>G (chr9-135106960-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001282611.2(OLFM1):c.783+105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 898,838 control chromosomes in the GnomAD database, including 8,264 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1639 hom., cov: 34)

Exomes 𝑓: 0.13 ( 6625 hom. )

Consequence

OLFM1
NM_001282611.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.10

Publications

2 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282611.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OLFM1	NM_001282611.2	MANE Select	c.783+105A>G	intron	N/A	NP_001269540.1	Q99784-1
OLFM1	NM_001282612.1		c.702+105A>G	intron	N/A	NP_001269541.1	Q99784-5
OLFM1	NM_014279.7		c.699+105A>G	intron	N/A	NP_055094.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OLFM1	ENST00000371793.8	TSL:3 MANE Select	c.783+105A>G	intron	N/A	ENSP00000360858.3	Q99784-1
OLFM1	ENST00000252854.8	TSL:1	c.729+105A>G	intron	N/A	ENSP00000252854.4	Q99784-3
OLFM1	ENST00000483042.1	TSL:1	n.1216+105A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21177

AN:

152138

Hom.:

1638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.0923

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0730

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.125

AC:

93384

AN:

746582

Hom.:

6625

AF XY:

0.122

AC XY:

46490

AN XY:

379562

show subpopulations

African (AFR)

AF:

0.181

AC:

3385

AN:

18746

American (AMR)

AF:

0.0828

AC:

2227

AN:

26890

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

2064

AN:

17028

East Asian (EAS)

AF:

0.00333

AC:

108

AN:

32386

South Asian (SAS)

AF:

0.0788

AC:

4437

AN:

56338

European-Finnish (FIN)

AF:

0.171

AC:

5365

AN:

31432

Middle Eastern (MID)

AF:

0.107

AC:

390

AN:

3632

European-Non Finnish (NFE)

AF:

0.136

AC:

71044

AN:

524082

Other (OTH)

AF:

0.121

AC:

4364

AN:

36048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4018

8036

12053

16071

20089

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1770

3540

5310

7080

8850

<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:

0.139

AC:

21194

AN:

152256

Hom.:

1639

Cov.:

AF XY:

0.136

AC XY:

10111

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.176

AC:

7310

AN:

41550

American (AMR)

AF:

0.0922

AC:

1411

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

406

AN:

3472

East Asian (EAS)

AF:

0.00232

AC:

AN:

5172

South Asian (SAS)

AF:

0.0735

AC:

355

AN:

4832

European-Finnish (FIN)

AF:

0.160

AC:

1697

AN:

10614

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.140

AC:

9512

AN:

67998

Other (OTH)

AF:

0.127

AC:

268

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

967

1934

2902

3869

4836

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.137

Hom.:

742

Bravo

AF:

0.137

Asia WGS

AF:

0.0420

AC:

149

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.15

(source)

DANN

Benign

0.67

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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