ENST00000371799.8:c.450_453dupCACA

Variant names:

• chr9-135077150-G-GCACA
• rs147807021
• ENST00000371799.8:c.450_453dupCACA

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

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]

ACMG classification

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	c.96+1363_96+1366dupCACA		intron_variant	Intron 1 of 5		NP_055094.1
OLFM1	NM_006334.4	c.96+1363_96+1366dupCACA		intron_variant	Intron 1 of 3		NP_006325.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00220 AC: 332 AN: 151180 Hom.: 2 Cov.: 32

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: 80 AN: 110262 Hom.: 0 AF XY: 0.000584 AC XY: 34 AN XY: 58244

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.: 0 Cov.: 34 AF XY: 0.000235 AC XY: 157 AN XY: 669102

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.: 2 Cov.: 32 AF XY: 0.00227 AC XY: 168 AN XY: 73902

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs147807021; hg19: chr9-137968996;