dbSNP rs13205210: BLTP3A:p.Met1098Thr (chr6-34864079-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 NM_017754.4(BLTP3A):c.3293T>C(p.Met1098Thr) variant causes a missense change. The variant allele was found at a frequency of 0.111 in 1,613,362 control chromosomes in the GnomAD database, including 10,672 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. M1098V) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.13 ( 1537 hom., cov: 31)

Exomes 𝑓: 0.11 ( 9135 hom. )

Consequence

BLTP3A
NM_017754.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.01

Publications

33 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017387867).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLTP3A	NM_017754.4 link	c.3293T>C	p.Met1098Thr	missense_variant	Exon 15 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.3293T>C	p.Met1098Thr	missense_variant	Exon 15 of 21	1	NM_017754.4	ENSP00000192788.5		Q6BDS2

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20172

AN:

151910

Hom.:

1529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0626

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.154

GnomAD2 exomes

AF:

0.111

AC:

27725

AN:

249218

AF XY:

0.113

show subpopulations

Gnomad AFR exome

AF:

0.205

Gnomad AMR exome

AF:

0.0817

Gnomad ASJ exome

AF:

0.183

Gnomad EAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.0587

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.108

AC:

158452

AN:

1461334

Hom.:

9135

Cov.:

AF XY:

0.109

AC XY:

79558

AN XY:

726944

show subpopulations

African (AFR)

AF:

0.202

AC:

6759

AN:

33468

American (AMR)

AF:

0.0839

AC:

3749

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.185

AC:

4829

AN:

26104

East Asian (EAS)

AF:

0.0894

AC:

3549

AN:

39686

South Asian (SAS)

AF:

0.119

AC:

10258

AN:

86138

European-Finnish (FIN)

AF:

0.0584

AC:

3120

AN:

53410

Middle Eastern (MID)

AF:

0.198

AC:

1140

AN:

5768

European-Non Finnish (NFE)

AF:

0.106

AC:

117603

AN:

1111684

Other (OTH)

AF:

0.123

AC:

7445

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

7284

14568

21853

29137

36421

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.133

AC:

20205

AN:

152028

Hom.:

1537

Cov.:

AF XY:

0.132

AC XY:

9842

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.202

AC:

8377

AN:

41426

American (AMR)

AF:

0.116

AC:

1779

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

598

AN:

3470

East Asian (EAS)

AF:

0.117

AC:

607

AN:

5178

South Asian (SAS)

AF:

0.115

AC:

552

AN:

4816

European-Finnish (FIN)

AF:

0.0626

AC:

662

AN:

10578

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7234

AN:

67954

Other (OTH)

AF:

0.155

AC:

326

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

883

1766

2648

3531

4414

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.121

Hom.:

5641

Bravo

AF:

0.142

TwinsUK

AF:

0.115

AC:

428

ALSPAC

AF:

0.102

AC:

393

ESP6500AA

AF:

0.193

AC:

778

ESP6500EA

AF:

0.111

AC:

924

ExAC

AF:

0.114

AC:

13759

Asia WGS

AF:

0.133

AC:

463

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.38

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.21

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.27

T;T

Eigen

Uncertain

0.38

Eigen_PC

Uncertain

0.49

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Benign

0.85

D;D

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.7

.;M

PhyloP100

7.0

PrimateAI

Uncertain

0.72

PROVEAN

Uncertain

-4.2

D;D

REVEL

Benign

0.27

Sift

Uncertain

0.0030

D;D

Sift4G

Uncertain

0.0020

D;D

Polyphen

0.83

.;P

Vest4

0.24

MPC

0.52

ClinPred

0.036

GERP RS

6.0

Varity_R

0.61

gMVP

0.58

Mutation Taster

=82/18

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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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rs13205210

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