Variant rs4907956 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_058170.4(OLFM3):c.70-10122C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 748,190 control chromosomes in the GnomAD database, including 51,440 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 0.26 ( 6517 hom., cov: 32)

Exomes 𝑓: 0.38 ( 44923 hom. )

Consequence

OLFM3
NM_058170.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318

Variant links:

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]

OLFM3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
OLFM3	NM_058170.4 linkuse as main transcript	c.70-10122C>A	intron_variant	ENST00000370103.9
OLFM3	NM_001288823.2 linkuse as main transcript	c.-156-10122C>A	intron_variant
OLFM3	NR_110210.2 linkuse as main transcript	n.241-10122C>A	intron_variant, non_coding_transcript_variant
OLFM3	NR_110211.2 linkuse as main transcript	n.180-10122C>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
OLFM3	ENST00000370103.9 linkuse as main transcript	c.70-10122C>A	intron_variant	1	NM_058170.4	P4	Q96PB7-3
OLFM3	ENST00000462354.5 linkuse as main transcript	n.159-10122C>A	intron_variant, non_coding_transcript_variant	1
OLFM3	ENST00000468901.1 linkuse as main transcript	n.120-9249C>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39134

AN:

151992

Hom.:

6515

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0742

Gnomad AMI

AF:

0.234

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.0119

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.381

AC:

227123

AN:

596080

Hom.:

44923

AF XY:

0.381

AC XY:

106132

AN XY:

278280

show subpopulations

Gnomad4 AFR exome

AF:

0.0460

Gnomad4 AMR exome

AF:

0.251

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.0131

Gnomad4 SAS exome

AF:

0.237

Gnomad4 FIN exome

AF:

0.303

Gnomad4 NFE exome

AF:

0.394

Gnomad4 OTH exome

AF:

0.339

GnomAD4 genome

AF:

0.257

AC:

39139

AN:

152110

Hom.:

6517

Cov.:

AF XY:

0.252

AC XY:

18747

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0740

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.0118

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.360

Hom.:

16171

Bravo

AF:

0.246

Asia WGS

AF:

0.120

AC:

418

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.76

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over