Variant 9-135077150-GCACA-GCACACACA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000371799.8(OLFM1):c.450_453dupCACA(p.Cys152HisfsTer42) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00048 in 1,509,186 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0022 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00029 ( 0 hom. )

Consequence

OLFM1
ENST00000371799.8 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.399

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 made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM1	NM_014279.5 link	c.96+1363_96+1366dupCACA		intron_variant	Intron 1 of 5		NP_055094.1	Q99784-3Q6IMJ8
OLFM1	NM_006334.4 link	c.96+1363_96+1366dupCACA		intron_variant	Intron 1 of 3		NP_006325.1	Q99784-4Q6IMJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
OLFM1	ENST00000371799.8 link	c.450_453dupCACA	p.Cys152HisfsTer42	frameshift_variant	Exon 2 of 2	1	ENSP00000360864.4	Q6IMJ6
OLFM1	ENST00000252854.8 link	c.96+1363_96+1366dupCACA		intron_variant	Intron 1 of 5	1	ENSP00000252854.4	Q99784-3
OLFM1	ENST00000277415.15 link	c.96+1363_96+1366dupCACA		intron_variant	Intron 1 of 3	1	ENSP00000277415.11	Q99784-4

Frequencies

GnomAD3 genomes

AF:

0.00220

AC:

332

AN:

151180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00722

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00165

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00645

Gnomad NFE

AF:

0.0000886

Gnomad OTH

AF:

0.000964

GnomAD3 exomes

AF:

0.000726

AC:

AN:

110262

Hom.:

AF XY:

0.000584

AC XY:

AN XY:

58244

show subpopulations

Gnomad AFR exome

AF:

0.00813

Gnomad AMR exome

AF:

0.000775

Gnomad ASJ exome

AF:

0.000182

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000646

Gnomad FIN exome

AF:

0.0000916

Gnomad NFE exome

AF:

0.000125

Gnomad OTH exome

AF:

0.00179

GnomAD4 exome

AF:

0.000289

AC:

392

AN:

1357900

Hom.:

Cov.:

AF XY:

0.000235

AC XY:

157

AN XY:

669102

show subpopulations

Gnomad4 AFR exome

AF:

0.00766

Gnomad4 AMR exome

AF:

0.000839

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000394

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000885

Gnomad4 OTH exome

AF:

0.000552

GnomAD4 genome

AF:

0.00219

AC:

332

AN:

151286

Hom.:

Cov.:

AF XY:

0.00227

AC XY:

168

AN XY:

73902

show subpopulations

Gnomad4 AFR

AF:

0.00720

Gnomad4 AMR

AF:

0.00164

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000886

Gnomad4 OTH

AF:

0.000955

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over