rs769163

Positions:

• chr1-101838596-T-C

Variant summary

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

The NM_058170.4(OLFM3):​c.70-1571A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,014 control chromosomes in the GnomAD database, including 24,028 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 0.54 (24028 hom., cov: 31)
• Consequence: OLFM3 NM_058170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFM3	NM_058170.4	c.70-1571A>G		intron_variant		ENST00000370103.9	NP_477518.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFM3	ENST00000370103.9	c.70-1571A>G		intron_variant		1	NM_058170.4	ENSP00000359121	P4

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82657 AN: 151896 Hom.: 24028 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.544 AC: 82689 AN: 152014 Hom.: 24028 Cov.: 31 AF XY: 0.548 AC XY: 40695 AN XY: 74306

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.546

Alfa AF: 0.612 Hom.: 45538

Bravo AF: 0.515

Asia WGS AF: 0.539 AC: 1872 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	3.1
DANN	Benign	0.76

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: rs769163; hg19: chr1-102304152;