rs11790027

Positions:

• chr9-135116397-C-T

Variant summary

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

The NM_001282611.2(OLFM1):​c.784-3107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,014 control chromosomes in the GnomAD database, including 1,933 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 (1933 hom., cov: 32)
• Consequence: OLFM1 NM_001282611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OLFM1	NM_001282611.2	c.784-3107C>T		intron_variant		ENST00000371793.8
OLFM1	NM_001282612.1	c.703-3107C>T		intron_variant
OLFM1	NM_014279.5	c.730-3107C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLFM1	ENST00000371793.8	c.784-3107C>T		intron_variant		3	NM_001282611.2	P1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22779 AN: 151896 Hom.: 1926 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.150 AC: 22818 AN: 152014 Hom.: 1933 Cov.: 32 AF XY: 0.151 AC XY: 11230 AN XY: 74302

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.142

Alfa AF: 0.119 Hom.: 2015

Bravo AF: 0.155

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
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: rs11790027; hg19: chr9-138008243;