1-101855259-C-G

Variant names:

• chr1-101855259-C-G
• rs962901
• NM_058170.4:c.70-18234G>C

Variant summary

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

The NM_058170.4(OLFM3):​c.70-18234G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 151,968 control chromosomes in the GnomAD database, including 879 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 0.067 (879 hom., cov: 32)
• Consequence: OLFM3 NM_058170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFM3	NM_058170.4	c.70-18234G>C		intron_variant	Intron 1 of 5	ENST00000370103.9	NP_477518.2
OLFM3	NM_001288823.2	c.-156-18234G>C		intron_variant	Intron 2 of 6		NP_001275752.1
OLFM3	NR_110210.2	n.241-18234G>C		intron_variant	Intron 2 of 7
OLFM3	NR_110211.2	n.180-18234G>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFM3	ENST00000370103.9	c.70-18234G>C		intron_variant	Intron 1 of 5	1	NM_058170.4	ENSP00000359121.5
OLFM3	ENST00000462354.5	n.159-18234G>C		intron_variant	Intron 1 of 6	1
OLFM3	ENST00000468901.1	n.120-17361G>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10133 AN: 151850 Hom.: 868 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0117

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00527

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0670 AC: 10178 AN: 151968 Hom.: 879 Cov.: 32 AF XY: 0.0696 AC XY: 5173 AN XY: 74274

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0117

Gnomad4 NFE AF: 0.00526

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.00440 Hom.: 3

Bravo AF: 0.0752

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.61

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: rs962901; hg19: chr1-102320815;