NM_058170.4:c.70-30408G>C

Variant names:

• chr1-101867433-C-G
• rs17125624
• NM_058170.4:c.70-30408G>C

Variant summary

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

The NM_058170.4(OLFM3):​c.70-30408G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,078 control chromosomes in the GnomAD database, including 1,087 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 0.11 (1087 hom., cov: 32)
• Consequence: OLFM3 NM_058170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_058170.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM3	NM_058170.4	MANE Select	c.70-30408G>C		intron	N/A	NP_477518.2	Q96PB7-3
	OLFM3	NM_001288823.2		c.-156-30408G>C		intron	N/A	NP_001275752.1	Q96PB7-5
	OLFM3	NR_110210.2		n.241-30408G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM3	ENST00000370103.9	TSL:1 MANE Select	c.70-30408G>C		intron	N/A	ENSP00000359121.5	Q96PB7-3
	OLFM3	ENST00000462354.5	TSL:1	n.159-30408G>C		intron	N/A
	OLFM3	ENST00000882547.1		c.70-30408G>C		intron	N/A	ENSP00000552606.1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17422 AN: 151960 Hom.: 1087 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.115 AC: 17420 AN: 152078 Hom.: 1087 Cov.: 32 AF XY: 0.112 AC XY: 8333 AN XY: 74342

African (AFR) AF: 0.125 AC: 5172 AN: 41482

American (AMR) AF: 0.0516 AC: 789 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1961 AN: 10554

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8715 AN: 67982

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0651 Hom.: 71

Bravo AF: 0.105

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.042
DANN	Benign	0.42
PhyloP100		-1.1
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: rs17125624; hg19: chr1-102332989;