9-135077150-GCA-G

Position:

• chr9-135077150-GCA-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The ENST00000371799.8(OLFM1):​c.452_453del​(p.Thr151MetfsTer41) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,390,134 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0018 (0 hom.)
• Consequence: OLFM1 ENST00000371799.8 frameshift
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 9-135077150-GCA-G is Benign according to our data. Variant chr9-135077150-GCA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2673203.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFM1	NM_006334.4	c.96+1365_96+1366del		intron_variant			NP_006325.1
OLFM1	NM_014279.5	c.96+1365_96+1366del		intron_variant			NP_055094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFM1	ENST00000371799.8	c.452_453del	p.Thr151MetfsTer41	frameshift_variant	2/2	1		ENSP00000360864
OLFM1	ENST00000252854.8	c.96+1365_96+1366del		intron_variant		1		ENSP00000252854
OLFM1	ENST00000277415.15	c.96+1365_96+1366del		intron_variant		1		ENSP00000277415

Frequencies

GnomAD3 genomes AF: 0.000126 AC: 19 AN: 151076 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000122

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.000629

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0130 AC: 1438 AN: 110262 Hom.: 0 AF XY: 0.0142 AC XY: 826 AN XY: 58244

Gnomad AFR exome AF: 0.00271

Gnomad AMR exome AF: 0.00997

Gnomad ASJ exome AF: 0.0199

Gnomad EAS exome AF: 0.00473

Gnomad SAS exome AF: 0.0207

Gnomad FIN exome AF: 0.0101

Gnomad NFE exome AF: 0.0153

Gnomad OTH exome AF: 0.0104

GnomAD4 exome AF: 0.00183 AC: 2264 AN: 1238952 Hom.: 0 AF XY: 0.00216 AC XY: 1313 AN XY: 609238

Gnomad4 AFR exome AF: 0.000935

Gnomad4 AMR exome AF: 0.00691

Gnomad4 ASJ exome AF: 0.00515

Gnomad4 EAS exome AF: 0.00282

Gnomad4 SAS exome AF: 0.00709

Gnomad4 FIN exome AF: 0.00345

Gnomad4 NFE exome AF: 0.00116

Gnomad4 OTH exome AF: 0.00179

GnomAD4 genome AF: 0.000126 AC: 19 AN: 151182 Hom.: 0 Cov.: 32 AF XY: 0.000122 AC XY: 9 AN XY: 73842

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000779

Gnomad4 SAS AF: 0.000629

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

OLFM1: BS1 -

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;