Variant rs12805648 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_198474.4(OLFML1):c.338A>T(p.Glu113Val) variant causes a missense change. The variant allele was found at a frequency of 0.176 in 1,613,724 control chromosomes in the GnomAD database, including 25,534 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 2219 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23315 hom. )

Consequence

OLFML1
NM_198474.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.95

Variant links:

Genes affected

OLFML1 (HGNC:24473): (olfactomedin like 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

OLFML1 links:

SYT9-AS1 (HGNC:56173): (SYT9 antisense RNA 1)

SYT9-AS1 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 (MetaRNN=0.0016070008).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFML1	NM_198474.4 linkuse as main transcript	c.338A>T	p.Glu113Val	missense_variant	2/3	ENST00000329293.4	NP_940876.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFML1	ENST00000329293.4 linkuse as main transcript	c.338A>T	p.Glu113Val	missense_variant	2/3	1	NM_198474.4	ENSP00000332511	P1
SYT9-AS1	ENST00000530201.2 linkuse as main transcript	n.1350+23788T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25279

AN:

152000

Hom.:

2217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.158

GnomAD3 exomes

AF:

0.182

AC:

45695

AN:

251092

Hom.:

4496

AF XY:

0.178

AC XY:

24170

AN XY:

135692

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.267

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.166

Gnomad SAS exome

AF:

0.142

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.174

Gnomad OTH exome

AF:

0.178

GnomAD4 exome

AF:

0.177

AC:

258583

AN:

1461606

Hom.:

23315

Cov.:

AF XY:

0.175

AC XY:

127550

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.128

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.162

Gnomad4 EAS exome

AF:

0.169

Gnomad4 SAS exome

AF:

0.143

Gnomad4 FIN exome

AF:

0.209

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.166

AC:

25307

AN:

152118

Hom.:

2219

Cov.:

AF XY:

0.170

AC XY:

12644

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.133

Gnomad4 AMR

AF:

0.214

Gnomad4 ASJ

AF:

0.173

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.148

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.168

Hom.:

1688

Bravo

AF:

0.165

TwinsUK

AF:

0.176

AC:

652

ALSPAC

AF:

0.176

AC:

679

ESP6500AA

AF:

0.132

AC:

579

ESP6500EA

AF:

0.169

AC:

1455

ExAC

AF:

0.177

AC:

21513

Asia WGS

AF:

0.165

AC:

575

AN:

3478

EpiCase

AF:

0.166

EpiControl

AF:

0.163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Uncertain

-0.080

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.023

T;T

Eigen

Benign

-0.0073

Eigen_PC

Benign

0.090

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.50

.;T

MetaRNN

Benign

0.0016

T;T

MetaSVM

Benign

-0.92

MutationAssessor

Uncertain

2.2

M;M

MutationTaster

Benign

0.66

P;P;P

PrimateAI

Benign

0.43

PROVEAN

Uncertain

-3.5

D;D

REVEL

Uncertain

0.39

Sift

Uncertain

0.011

D;D

Sift4G

Uncertain

0.0090

D;D

Polyphen

0.060

B;B

Vest4

0.28

MPC

0.022

ClinPred

0.024

GERP RS

5.7

Varity_R

0.26

gMVP

0.45

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