rs10874518

Positions:

• chr1-101806756-C-A
• chr1-101806756-C-G

Variant summary

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

The NM_058170.4(OLFM3):​c.593-574G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,558 control chromosomes in the GnomAD database, including 31,412 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 0.64 (31412 hom., cov: 31)
• Consequence: OLFM3 NM_058170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFM3	NM_058170.4	c.593-574G>T		intron_variant		ENST00000370103.9	NP_477518.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFM3	ENST00000370103.9	c.593-574G>T		intron_variant		1	NM_058170.4	ENSP00000359121	P4

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97180 AN: 151440 Hom.: 31398 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.642 AC: 97247 AN: 151558 Hom.: 31412 Cov.: 31 AF XY: 0.640 AC XY: 47408 AN XY: 74046

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.594

Alfa AF: 0.628 Hom.: 22884

Bravo AF: 0.636

Asia WGS AF: 0.534 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.015
DANN	Benign	0.23

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: rs10874518; hg19: chr1-102272312;