chr9-135106960-A-G

Variant names:

• chr9-135106960-A-G
• rs9969691
• NM_001282611.2:c.783+105A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
OLFM1	NM_001282611.2	c.783+105A>G		intron_variant	Intron 5 of 5	ENST00000371793.8	NP_001269540.1
OLFM1	NM_001282612.1	c.702+105A>G		intron_variant	Intron 5 of 5		NP_001269541.1
OLFM1	NM_014279.7	c.699+105A>G		intron_variant	Intron 5 of 5		NP_055094.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFM1	ENST00000371793.8	c.783+105A>G		intron_variant	Intron 5 of 5	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

African (AFR) AF: 0.181 AC: 3385 AN: 18746

American (AMR) AF: 0.0828 AC: 2227 AN: 26890

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 2064 AN: 17028

East Asian (EAS) AF: 0.00333 AC: 108 AN: 32386

South Asian (SAS) AF: 0.0788 AC: 4437 AN: 56338

European-Finnish (FIN) AF: 0.171 AC: 5365 AN: 31432

Middle Eastern (MID) AF: 0.107 AC: 390 AN: 3632

European-Non Finnish (NFE) AF: 0.136 AC: 71044 AN: 524082

Other (OTH) AF: 0.121 AC: 4364 AN: 36048

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

African (AFR) AF: 0.176 AC: 7310 AN: 41550

American (AMR) AF: 0.0922 AC: 1411 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5172

South Asian (SAS) AF: 0.0735 AC: 355 AN: 4832

European-Finnish (FIN) AF: 0.160 AC: 1697 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9512 AN: 67998

Other (OTH) AF: 0.127 AC: 268 AN: 2116

Alfa AF: 0.137 Hom.: 742

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
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9969691; hg19: chr9-137998806;