rs716581

chr1-101874077-G-A

Variant summary

Our verdict is Benign. Variant got -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

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OLFM3	NM_058170.4	c.70-37052C>T		intron_variant		ENST00000370103.9
DNAJA1P5	NR_033424.2	n.94+1972G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLFM3	ENST00000370103.9	c.70-37052C>T		intron_variant		1	NM_058170.4	P4
OLFM3	ENST00000462354.5	n.159-37052C>T		intron_variant, non_coding_transcript_variant		1
OLFM3	ENST00000468901.1	n.119+35959C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.505

Alfa AF: 0.531 Hom.: 9981

Bravo AF: 0.505

Asia WGS AF: 0.366 AC: 1267 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.2
Dann	Benign	0.84

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: rs716581; hg19: chr1-102339633;