rs1445225

Variant names:

• chr1-101819933-C-T
• rs1445225
• NM_058170.4:c.592+5093G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_058170.4(OLFM3):​c.592+5093G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,674 control chromosomes in the GnomAD database, including 19,714 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 0.51 (19714 hom., cov: 31)
• Consequence: OLFM3 NM_058170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 3 publications found

Genes affected

OLFM3 (HGNC:17990): (olfactomedin 3) Predicted to be involved in eye photoreceptor cell development. Predicted to be located in Golgi apparatus; extracellular space; and synapse. Predicted to be part of AMPA glutamate receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM3	NM_058170.4	c.592+5093G>A		intron_variant	Intron 4 of 5	ENST00000370103.9	NP_477518.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFM3	ENST00000370103.9	c.592+5093G>A		intron_variant	Intron 4 of 5	1	NM_058170.4	ENSP00000359121.5

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76751 AN: 151556 Hom.: 19707 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.506 AC: 76796 AN: 151674 Hom.: 19714 Cov.: 31 AF XY: 0.508 AC XY: 37625 AN XY: 74104

African (AFR) AF: 0.424 AC: 17507 AN: 41310

American (AMR) AF: 0.475 AC: 7220 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3286 AN: 5150

South Asian (SAS) AF: 0.513 AC: 2475 AN: 4822

European-Finnish (FIN) AF: 0.613 AC: 6455 AN: 10536

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36298 AN: 67870

Other (OTH) AF: 0.494 AC: 1043 AN: 2110

Alfa AF: 0.525 Hom.: 62499

Bravo AF: 0.495

Asia WGS AF: 0.535 AC: 1860 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	2.1
DANN	Benign	0.26
PhyloP100		-0.13
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: rs1445225; hg19: chr1-102285489;