dbSNP rs4907956: OLFM3:c.70-10122C>A (chr1-101847147-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_058170.4(OLFM3):c.70-10122C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 748,190 control chromosomes in the GnomAD database, including 51,440 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 0.26 ( 6517 hom., cov: 32)

Exomes 𝑓: 0.38 ( 44923 hom. )

Consequence

OLFM3
NM_058170.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318

Publications

5 publications found

Variant links:

Genes affected

OLFM3 (HGNC:17990): (olfactomedin 3) Predicted to be involved in eye photoreceptor cell development. Predicted to be located in Golgi apparatus; extracellular space; and synapse. Predicted to be part of AMPA glutamate receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

OLFM3 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=-0.57).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_058170.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
OLFM3	NM_058170.4	MANE Select	c.70-10122C>A	intron	N/A	NP_477518.2
OLFM3	NM_001288823.2		c.-156-10122C>A	intron	N/A	NP_001275752.1
OLFM3	NR_110210.2		n.241-10122C>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
OLFM3	ENST00000370103.9	TSL:1 MANE Select	c.70-10122C>A	intron	N/A	ENSP00000359121.5
OLFM3	ENST00000462354.5	TSL:1	n.159-10122C>A	intron	N/A
OLFM3	ENST00000882547.1		c.70-10122C>A	intron	N/A	ENSP00000552606.1

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39134

AN:

151992

Hom.:

6515

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0742

Gnomad AMI

AF:

0.234

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.0119

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.381

AC:

227123

AN:

596080

Hom.:

44923

AF XY:

0.381

AC XY:

106132

AN XY:

278280

show subpopulations

African (AFR)

AF:

0.0460

AC:

507

AN:

11018

American (AMR)

AF:

0.251

AC:

170

AN:

678

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

1416

AN:

3674

East Asian (EAS)

AF:

0.0131

AC:

AN:

2452

South Asian (SAS)

AF:

0.237

AC:

2771

AN:

11704

European-Finnish (FIN)

AF:

0.303

AC:

AN:

208

Middle Eastern (MID)

AF:

0.299

AC:

355

AN:

1188

European-Non Finnish (NFE)

AF:

0.394

AC:

215240

AN:

545772

Other (OTH)

AF:

0.339

AC:

6569

AN:

19386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

6542

13084

19625

26167

32709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9060

18120

27180

36240

45300

<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:

0.257

AC:

39139

AN:

152110

Hom.:

6517

Cov.:

AF XY:

0.252

AC XY:

18747

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0740

AC:

3073

AN:

41508

American (AMR)

AF:

0.258

AC:

3945

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1232

AN:

3468

East Asian (EAS)

AF:

0.0118

AC:

AN:

5182

South Asian (SAS)

AF:

0.222

AC:

1073

AN:

4828

European-Finnish (FIN)

AF:

0.291

AC:

3073

AN:

10568

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.379

AC:

25752

AN:

67966

Other (OTH)

AF:

0.294

AC:

620

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1367

2734

4101

5468

6835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.354

Hom.:

29060

Bravo

AF:

0.246

Asia WGS

AF:

0.120

AC:

418

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.32

PromoterAI

-0.026

Neutral

(source)

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