rs9969691

Positions:

• chr9-135106960-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001282611.2(OLFM1):​c.783+105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 898,838 control chromosomes in the GnomAD database, including 8,264 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.14 (1639 hom., cov: 34)
  • Exomes 𝑓: 0.13 (6625 hom.)
• Consequence: OLFM1 NM_001282611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFM1	NM_001282611.2	c.783+105A>G		intron_variant		ENST00000371793.8	NP_001269540.1
OLFM1	NM_014279.5	c.729+105A>G		intron_variant			NP_055094.1
OLFM1	NM_001282612.1	c.702+105A>G		intron_variant			NP_001269541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFM1	ENST00000371793.8	c.783+105A>G		intron_variant		3	NM_001282611.2	ENSP00000360858.3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21177 AN: 152138 Hom.: 1638 Cov.: 34

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.125 AC: 93384 AN: 746582 Hom.: 6625 AF XY: 0.122 AC XY: 46490 AN XY: 379562

Gnomad4 AFR exome AF: 0.181

Gnomad4 AMR exome AF: 0.0828

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.00333

Gnomad4 SAS exome AF: 0.0788

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.139 AC: 21194 AN: 152256 Hom.: 1639 Cov.: 34 AF XY: 0.136 AC XY: 10111 AN XY: 74450

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0922

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.127

Alfa AF: 0.137 Hom.: 676

Bravo AF: 0.137

Asia WGS AF: 0.0420 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9969691; hg19: chr9-137998806;