chr1-101806756-C-A

Variant names:

• chr1-101806756-C-A
• rs10874518
• NM_058170.4:c.593-574G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.95).
• 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 rank	MANE	Protein	UniProt
OLFM3	NM_058170.4	c.593-574G>T		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.593-574G>T		intron_variant	Intron 4 of 5	1	NM_058170.4	ENSP00000359121.5

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

African (AFR) AF: 0.638 AC: 26390 AN: 41380

American (AMR) AF: 0.615 AC: 9329 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2111 AN: 3462

East Asian (EAS) AF: 0.654 AC: 3349 AN: 5122

South Asian (SAS) AF: 0.485 AC: 2335 AN: 4812

European-Finnish (FIN) AF: 0.733 AC: 7751 AN: 10576

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43850 AN: 67722

Other (OTH) AF: 0.594 AC: 1249 AN: 2104

Alfa AF: 0.630 Hom.: 31322

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
PhyloP100		-2.6
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: rs10874518; hg19: chr1-102272312;