chr1-101855259-C-G

Variant names:

• chr1-101855259-C-G
• rs962901
• NM_058170.4:c.70-18234G>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.70-18234G>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
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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.70-18234G>C		intron	N/A	NP_477518.2	Q96PB7-3
	OLFM3	NM_001288823.2		c.-156-18234G>C		intron	N/A	NP_001275752.1	Q96PB7-5
	OLFM3	NR_110210.2		n.241-18234G>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.70-18234G>C		intron	N/A	ENSP00000359121.5	Q96PB7-3
	OLFM3	ENST00000462354.5	TSL:1	n.159-18234G>C		intron	N/A
	OLFM3	ENST00000882547.1		c.70-18234G>C		intron	N/A	ENSP00000552606.1

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

African (AFR) AF: 0.158 AC: 6556 AN: 41456

American (AMR) AF: 0.0560 AC: 854 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3464

East Asian (EAS) AF: 0.326 AC: 1682 AN: 5152

South Asian (SAS) AF: 0.0821 AC: 396 AN: 4822

European-Finnish (FIN) AF: 0.0117 AC: 124 AN: 10598

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.00526 AC: 357 AN: 67920

Other (OTH) AF: 0.0640 AC: 135 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		-0.39
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: rs962901; hg19: chr1-102320815;