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

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3BS1BS2

The ENST00000371799.8(OLFM1):c.448_453dupCACACA(p.His150_Thr151dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,509,224 control chromosomes in the GnomAD database, including 26 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0096 ( 21 hom., cov: 32)

Exomes 𝑓: 0.00091 ( 5 hom. )

Consequence

OLFM1
ENST00000371799.8 conservative_inframe_insertion

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 Benign. Variant got -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in ENST00000371799.8

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00962 (1455/151282) while in subpopulation AFR AF= 0.0335 (1383/41248). AF 95% confidence interval is 0.0321. There are 21 homozygotes in gnomad4. There are 698 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM1	NM_014279.5 link	c.96+1361_96+1366dupCACACA		intron_variant	Intron 1 of 5		NP_055094.1	Q99784-3Q6IMJ8
OLFM1	NM_006334.4 link	c.96+1361_96+1366dupCACACA		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.448_453dupCACACA	p.His150_Thr151dup	conservative_inframe_insertion	Exon 2 of 2	1	ENSP00000360864.4	Q6IMJ6
OLFM1	ENST00000252854.8 link	c.96+1361_96+1366dupCACACA		intron_variant	Intron 1 of 5	1	ENSP00000252854.4	Q99784-3
OLFM1	ENST00000277415.15 link	c.96+1361_96+1366dupCACACA		intron_variant	Intron 1 of 3	1	ENSP00000277415.11	Q99784-4

Frequencies

GnomAD3 genomes

AF:

0.00962

AC:

1454

AN:

151176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0336

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00336

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00323

Gnomad NFE

AF:

0.0000738

Gnomad OTH

AF:

0.00676

GnomAD3 exomes

AF:

0.00222

AC:

245

AN:

110262

Hom.:

AF XY:

0.00179

AC XY:

104

AN XY:

58244

show subpopulations

Gnomad AFR exome

AF:

0.0327

Gnomad AMR exome

AF:

0.00186

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000251

Gnomad OTH exome

AF:

0.000894

GnomAD4 exome

AF:

0.000910

AC:

1236

AN:

1357942

Hom.:

Cov.:

AF XY:

0.000822

AC XY:

550

AN XY:

669124

show subpopulations

Gnomad4 AFR exome

AF:

0.0336

Gnomad4 AMR exome

AF:

0.00185

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000789

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000952

Gnomad4 OTH exome

AF:

0.00208

GnomAD4 genome

AF:

0.00962

AC:

1455

AN:

151282

Hom.:

Cov.:

AF XY:

0.00945

AC XY:

698

AN XY:

73898

show subpopulations

Gnomad4 AFR

AF:

0.0335

Gnomad4 AMR

AF:

0.00335

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000210

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000738

Gnomad4 OTH

AF:

0.00669

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