9-135077150-GCACACACACA-GCACA

Variant names:

• chr9-135077150-GCACACA-G
• rs147807021
• ENST00000371799.8:c.448_453delCACACA

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP3

The ENST00000371799.8(OLFM1):​c.448_453delCACACA​(p.His150_Thr151del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000515 in 1,357,938 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000052 (0 hom.)
• Consequence: OLFM1 ENST00000371799.8 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP3: Nonframeshift variant in repetitive region in ENST00000371799.8

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371799.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM1	NM_014279.7		c.66+1361_66+1366delCACACA		intron	N/A	NP_055094.2
	OLFM1	NM_006334.6		c.66+1361_66+1366delCACACA		intron	N/A	NP_006325.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM1	ENST00000371799.8	TSL:1	c.448_453delCACACA	p.His150_Thr151del	conservative_inframe_deletion	Exon 2 of 2	ENSP00000360864.4	Q6IMJ6
	OLFM1	ENST00000252854.8	TSL:1	c.96+1361_96+1366delCACACA		intron	N/A	ENSP00000252854.4	Q99784-3
	OLFM1	ENST00000277415.15	TSL:1	c.96+1361_96+1366delCACACA		intron	N/A	ENSP00000277415.11	Q99784-4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000515 AC: 7 AN: 1357938 Hom.: 0 AF XY: 0.00000747 AC XY: 5 AN XY: 669122

African (AFR) AF: 0.00 AC: 0 AN: 30712

American (AMR) AF: 0.00 AC: 0 AN: 34558

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24128

East Asian (EAS) AF: 0.00 AC: 0 AN: 33928

South Asian (SAS) AF: 0.00 AC: 0 AN: 76064

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46364

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5544

European-Non Finnish (NFE) AF: 0.00000666 AC: 7 AN: 1050506

Other (OTH) AF: 0.00 AC: 0 AN: 56134

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs147807021; hg19: chr9-137968996;