Variant 6-34834333-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_017754.4(BLTP3A):c.455G>T(p.Gly152Val) variant causes a missense change. The variant allele was found at a frequency of 0.00141 in 1,613,974 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 20 hom. )

Consequence

BLTP3A
NM_017754.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.61

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010248005).

BP6

Variant 6-34834333-G-T is Benign according to our data. Variant chr6-34834333-G-T is described in ClinVar as [Benign]. Clinvar id is 711315.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP3A	NM_017754.4 linkuse as main transcript	c.455G>T	p.Gly152Val	missense_variant	5/21	ENST00000192788.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP3A	ENST00000192788.6 linkuse as main transcript	c.455G>T	p.Gly152Val	missense_variant	5/21	1	NM_017754.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00148

AC:

226

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000290

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.0135

Gnomad SAS

AF:

0.00476

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000926

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00344

AC:

859

AN:

249414

Hom.:

AF XY:

0.00379

AC XY:

513

AN XY:

135344

show subpopulations

Gnomad AFR exome

AF:

0.000129

Gnomad AMR exome

AF:

0.000811

Gnomad ASJ exome

AF:

0.00556

Gnomad EAS exome

AF:

0.0235

Gnomad SAS exome

AF:

0.00634

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00118

Gnomad OTH exome

AF:

0.00314

GnomAD4 exome

AF:

0.00140

AC:

2044

AN:

1461662

Hom.:

Cov.:

AF XY:

0.00162

AC XY:

1180

AN XY:

727148

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000939

Gnomad4 ASJ exome

AF:

0.00601

Gnomad4 EAS exome

AF:

0.00743

Gnomad4 SAS exome

AF:

0.00642

Gnomad4 FIN exome

AF:

0.000225

Gnomad4 NFE exome

AF:

0.000694

Gnomad4 OTH exome

AF:

0.00220

GnomAD4 genome

AF:

0.00148

AC:

226

AN:

152312

Hom.:

Cov.:

AF XY:

0.00158

AC XY:

118

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.0135

Gnomad4 SAS

AF:

0.00476

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.000926

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00119

Hom.:

Bravo

AF:

0.00186

ESP6500AA

AF:

0.000252

AC:

ESP6500EA

AF:

0.000722

AC:

ExAC

AF:

0.00341

AC:

412

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.00164

EpiControl

AF:

0.00154

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

May 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.28

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.39

Cadd

Pathogenic

Dann

Benign

0.40

DEOGEN2

Benign

0.0044

T;T

Eigen

Uncertain

0.31

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Uncertain

0.97

LIST_S2

Uncertain

0.87

D;D

MetaRNN

Benign

0.010

T;T

MetaSVM

Benign

-0.92

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.77

PROVEAN

Benign

0.68

N;N

REVEL

Uncertain

0.30

Sift

Benign

0.95

T;T

Sift4G

Benign

0.95

T;T

Polyphen

1.0

.;D

Vest4

0.59

MVP

0.68

MPC

0.59

ClinPred

0.056

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.21

gMVP

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over