rs11790742

Variant names:

• chr9-135116149-A-G
• rs11790742
• NM_001282611.2:c.784-3355A>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.784-3355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,184 control chromosomes in the GnomAD database, including 2,008 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 0.15 (2008 hom., cov: 32)
• Consequence: OLFM1 NM_001282611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM1	NM_001282611.2	c.784-3355A>G		intron_variant	Intron 5 of 5	ENST00000371793.8	NP_001269540.1
OLFM1	NM_001282612.1	c.703-3355A>G		intron_variant	Intron 5 of 5		NP_001269541.1
OLFM1	NM_014279.7	c.700-3355A>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.784-3355A>G		intron_variant	Intron 5 of 5	3	NM_001282611.2	ENSP00000360858.3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22988 AN: 152066 Hom.: 2001 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 23027 AN: 152184 Hom.: 2008 Cov.: 32 AF XY: 0.152 AC XY: 11338 AN XY: 74402

African (AFR) AF: 0.233 AC: 9660 AN: 41514

American (AMR) AF: 0.127 AC: 1949 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3466

East Asian (EAS) AF: 0.0728 AC: 376 AN: 5168

South Asian (SAS) AF: 0.110 AC: 532 AN: 4828

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7766 AN: 67998

Other (OTH) AF: 0.144 AC: 304 AN: 2114

Alfa AF: 0.123 Hom.: 711

Bravo AF: 0.156

Asia WGS AF: 0.104 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		-0.036
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: rs11790742; hg19: chr9-138007995;