1-161984140-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_015441.3(OLFML2B):ā€‹c.1788T>Cā€‹(p.Ala596Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00422 in 1,610,758 control chromosomes in the GnomAD database, including 236 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.023 ( 136 hom., cov: 32)
Exomes š‘“: 0.0023 ( 100 hom. )

Consequence

OLFML2B
NM_015441.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.71
Variant links:
Genes affected
OLFML2B (HGNC:24558): (olfactomedin like 2B) This gene encodes an olfactomedin domain-containing protein. Most olfactomedin domain-containing proteins are secreted glycoproteins. [provided by RefSeq, Dec 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-161984140-A-G is Benign according to our data. Variant chr1-161984140-A-G is described in ClinVar as [Benign]. Clinvar id is 780275.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.71 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OLFML2BNM_015441.3 linkc.1788T>C p.Ala596Ala synonymous_variant 8/8 ENST00000294794.8 NP_056256.1 Q68BL8-1
OLFML2BNM_001347700.2 linkc.1794T>C p.Ala598Ala synonymous_variant 8/8 NP_001334629.1
OLFML2BNM_001297713.2 linkc.1791T>C p.Ala597Ala synonymous_variant 8/8 NP_001284642.1 Q68BL8F2Z3N3B4DWE8
OLFML2BXM_011509398.3 linkc.1068T>C p.Ala356Ala synonymous_variant 5/5 XP_011507700.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OLFML2BENST00000294794.8 linkc.1788T>C p.Ala596Ala synonymous_variant 8/81 NM_015441.3 ENSP00000294794.3 Q68BL8-1
OLFML2BENST00000367940.2 linkc.1791T>C p.Ala597Ala synonymous_variant 8/82 ENSP00000356917.2 F2Z3N3
OLFML2BENST00000367938.1 linkc.237T>C p.Ala79Ala synonymous_variant 2/22 ENSP00000356915.1 Q68BL8-2

Frequencies

GnomAD3 genomes
AF:
0.0229
AC:
3487
AN:
152214
Hom.:
136
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0794
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00909
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.0181
GnomAD3 exomes
AF:
0.00585
AC:
1445
AN:
247106
Hom.:
45
AF XY:
0.00413
AC XY:
551
AN XY:
133514
show subpopulations
Gnomad AFR exome
AF:
0.0769
Gnomad AMR exome
AF:
0.00421
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000167
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000278
Gnomad OTH exome
AF:
0.00332
GnomAD4 exome
AF:
0.00227
AC:
3312
AN:
1458426
Hom.:
100
Cov.:
31
AF XY:
0.00194
AC XY:
1408
AN XY:
725194
show subpopulations
Gnomad4 AFR exome
AF:
0.0779
Gnomad4 AMR exome
AF:
0.00519
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000291
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000151
Gnomad4 OTH exome
AF:
0.00460
GnomAD4 genome
AF:
0.0229
AC:
3493
AN:
152332
Hom.:
136
Cov.:
32
AF XY:
0.0222
AC XY:
1652
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0793
Gnomad4 AMR
AF:
0.00908
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.0180
Alfa
AF:
0.0123
Hom.:
40
Bravo
AF:
0.0259
Asia WGS
AF:
0.00318
AC:
11
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 21, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
4.1
DANN
Benign
0.58

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.

Other links and lift over

dbSNP: rs61737578; hg19: chr1-161953930; API