Genetic Variant ENST00000399441.4:c.*71A>G (chr18-24358420-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000399441.4(OSBPL1A):c.*71A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 700,632 control chromosomes in the GnomAD database, including 120,320 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 0.62 ( 30069 hom., cov: 33)

Exomes 𝑓: 0.56 ( 90251 hom. )

Consequence

OSBPL1A
ENST00000399441.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193

Publications

5 publications found

Variant links:

Genes affected

OSBPL1A (HGNC:16398): (oxysterol binding protein like 1A) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain, although some members contain only the sterol-binding domain. Transcript variants derived from alternative promoter usage and/or alternative splicing exist; they encode different isoforms. [provided by RefSeq, Jul 2008]

OSBPL1A links:

LOC124904267 (HGNC:):

LOC124904267 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
OSBPL1A	NM_080597.4 link	c.282+8472A>G	intron_variant	Intron 4 of 27	ENST00000319481.8	NP_542164.2	Q9BXW6-1B0YJ56B3KU11
OSBPL1A	XM_017025530.2 link	c.336+8472A>G	intron_variant	Intron 4 of 27		XP_016881019.1
LOC124904267	XR_007066312.1 link	n.327-1572T>C	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL1A	ENST00000319481.8 link	c.282+8472A>G		intron_variant	Intron 4 of 27	1	NM_080597.4	ENSP00000320291.3		Q9BXW6-1

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93559

AN:

152014

Hom.:

30022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.782

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.650

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.843

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.512

Gnomad OTH

AF:

0.602

GnomAD4 exome

AF:

0.564

AC:

309578

AN:

548500

Hom.:

90251

Cov.:

AF XY:

0.562

AC XY:

166927

AN XY:

296978

show subpopulations

African (AFR)

AF:

0.784

AC:

12368

AN:

15768

American (AMR)

AF:

0.714

AC:

24599

AN:

34464

Ashkenazi Jewish (ASJ)

AF:

0.513

AC:

10212

AN:

19896

East Asian (EAS)

AF:

0.809

AC:

25981

AN:

32100

South Asian (SAS)

AF:

0.589

AC:

36790

AN:

62498

European-Finnish (FIN)

AF:

0.532

AC:

17633

AN:

33140

Middle Eastern (MID)

AF:

0.559

AC:

2207

AN:

3950

European-Non Finnish (NFE)

AF:

0.514

AC:

162417

AN:

316170

Other (OTH)

AF:

0.569

AC:

17371

AN:

30514

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

6910

13820

20731

27641

34551

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

900

1800

2700

3600

4500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.616

AC:

93664

AN:

152132

Hom.:

30069

Cov.:

AF XY:

0.617

AC XY:

45883

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.782

AC:

32456

AN:

41498

American (AMR)

AF:

0.650

AC:

9934

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1732

AN:

3472

East Asian (EAS)

AF:

0.843

AC:

4362

AN:

5174

South Asian (SAS)

AF:

0.596

AC:

2879

AN:

4832

European-Finnish (FIN)

AF:

0.533

AC:

5632

AN:

10576

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.512

AC:

34798

AN:

67980

Other (OTH)

AF:

0.596

AC:

1262

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1739

3478

5216

6955

8694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.545

Hom.:

13874

Bravo

AF:

0.637

Asia WGS

AF:

0.707

AC:

2458

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

(source)

DANN

Benign

0.57

PhyloP100

-0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over