1-101874077-G-A

Variant names:

• chr1-101874077-G-A
• rs716581
• NM_058170.4:c.70-37052C>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.70-37052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,648 control chromosomes in the GnomAD database, including 20,078 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 0.51 (20078 hom., cov: 32)
• Consequence: OLFM3 NM_058170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 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]

DNAJA1P5 (HGNC:39341): (DnaJ heat shock protein family (Hsp40) member A1 pseudogene 5)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM3	NM_058170.4	MANE Select	c.70-37052C>T		intron	N/A	NP_477518.2
	OLFM3	NM_001288823.2		c.-156-37052C>T		intron	N/A	NP_001275752.1
	DNAJA1P5	NR_033424.2		n.94+1972G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM3	ENST00000370103.9	TSL:1 MANE Select	c.70-37052C>T		intron	N/A	ENSP00000359121.5
	OLFM3	ENST00000462354.5	TSL:1	n.159-37052C>T		intron	N/A
	OLFM3	ENST00000468901.1	TSL:5	n.119+35959C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77141 AN: 151530 Hom.: 20054 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.509 AC: 77199 AN: 151648 Hom.: 20078 Cov.: 32 AF XY: 0.498 AC XY: 36929 AN XY: 74092

African (AFR) AF: 0.495 AC: 20528 AN: 41444

American (AMR) AF: 0.410 AC: 6240 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1952 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1803 AN: 5148

South Asian (SAS) AF: 0.341 AC: 1643 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5222 AN: 10540

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38028 AN: 67714

Other (OTH) AF: 0.505 AC: 1063 AN: 2106

Alfa AF: 0.535 Hom.: 11256

Bravo AF: 0.505

Asia WGS AF: 0.366 AC: 1267 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.84
PhyloP100		0.026
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: rs716581; hg19: chr1-102339633;