Genetic Variant BLTP3A:p.Leu579Leu (chr6-34857885-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017754.4(BLTP3A):c.1735T>C(p.Leu579Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,613,712 control chromosomes in the GnomAD database, including 17,853 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 0.17 ( 2597 hom., cov: 32)

Exomes 𝑓: 0.14 ( 15256 hom. )

Consequence

BLTP3A
NM_017754.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.431

Publications

32 publications found

Variant links:

Genes affected

BLTP3A (HGNC:21216): (bridge-like lipid transfer protein family member 3A) Enables histone deacetylase binding activity and identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

BLTP3A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-0.431 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLTP3A	NM_017754.4 link	c.1735T>C	p.Leu579Leu	synonymous_variant	Exon 13 of 21	ENST00000192788.6	NP_060224.3	Q6BDS2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLTP3A	ENST00000192788.6 link	c.1735T>C	p.Leu579Leu	synonymous_variant	Exon 13 of 21	1	NM_017754.4	ENSP00000192788.5		Q6BDS2

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26422

AN:

151990

Hom.:

2593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.0110

Gnomad SAS

AF:

0.0809

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.160

GnomAD2 exomes

AF:

0.131

AC:

32626

AN:

249234

AF XY:

0.129

show subpopulations

Gnomad AFR exome

AF:

0.252

Gnomad AMR exome

AF:

0.0802

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.0135

Gnomad FIN exome

AF:

0.211

Gnomad NFE exome

AF:

0.146

Gnomad OTH exome

AF:

0.133

GnomAD4 exome

AF:

0.138

AC:

202302

AN:

1461604

Hom.:

15256

Cov.:

AF XY:

0.137

AC XY:

99503

AN XY:

727082

show subpopulations

African (AFR)

AF:

0.260

AC:

8693

AN:

33478

American (AMR)

AF:

0.0860

AC:

3844

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

4077

AN:

26134

East Asian (EAS)

AF:

0.00658

AC:

261

AN:

39690

South Asian (SAS)

AF:

0.0772

AC:

6663

AN:

86258

European-Finnish (FIN)

AF:

0.204

AC:

10894

AN:

53272

Middle Eastern (MID)

AF:

0.129

AC:

744

AN:

5768

European-Non Finnish (NFE)

AF:

0.143

AC:

158774

AN:

1111894

Other (OTH)

AF:

0.138

AC:

8352

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

9401

18802

28203

37604

47005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5584

11168

16752

22336

27920

<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:

0.174

AC:

26440

AN:

152108

Hom.:

2597

Cov.:

AF XY:

0.175

AC XY:

12990

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.254

AC:

10546

AN:

41470

American (AMR)

AF:

0.124

AC:

1896

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

566

AN:

3470

East Asian (EAS)

AF:

0.0110

AC:

AN:

5182

South Asian (SAS)

AF:

0.0793

AC:

383

AN:

4828

European-Finnish (FIN)

AF:

0.214

AC:

2268

AN:

10578

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10188

AN:

67996

Other (OTH)

AF:

0.158

AC:

333

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1069

2138

3208

4277

5346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.154

Hom.:

2037

Bravo

AF:

0.172

Asia WGS

AF:

0.0490

AC:

172

AN:

3478

EpiCase

AF:

0.143

EpiControl

AF:

0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.77

(source)

DANN

Benign

0.53

PhyloP100

-0.43

Mutation Taster

=97/3

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