Variant 4-122174548-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001384125.1(BLTP1):c.215-26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 1,602,402 control chromosomes in the GnomAD database, including 1,791 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.064 ( 885 hom., cov: 32)

Exomes 𝑓: 0.014 ( 906 hom. )

Consequence

BLTP1
NM_001384125.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.486

Variant links:

Genes affected

BLTP1 (HGNC:26953): (bridge-like lipid transfer protein family member 1) This gene is located on the long arm of chromosome 4 in a region that is associated with susceptibility to celiac disease. The encoded protein is similar to a Chinese hamster protein that is associated with spermatocyte and adipocyte differentiation. The C-terminus of the protein is also similar to a Caenorhabditis elegans protein that plays a role in lipid storage. In mammals, this protein is thought to function in the regulation of epithelial growth and differentiation, and in tumor development. [provided by RefSeq, Oct 2009]

BLTP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 4-122174548-C-T is Benign according to our data. Variant chr4-122174548-C-T is described in ClinVar as [Benign]. Clinvar id is 1231351.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLTP1	NM_001384125.1 linkuse as main transcript	c.215-26C>T		intron_variant		ENST00000679879.1	NP_001371054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLTP1	ENST00000679879.1 linkuse as main transcript	c.215-26C>T		intron_variant			NM_001384125.1	ENSP00000505357	A2

Frequencies

GnomAD3 genomes

AF:

0.0641

AC:

9739

AN:

152012

Hom.:

881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00747

Gnomad OTH

AF:

0.0551

GnomAD3 exomes

AF:

0.0239

AC:

5760

AN:

240844

Hom.:

375

AF XY:

0.0208

AC XY:

2727

AN XY:

130868

show subpopulations

Gnomad AFR exome

AF:

0.213

Gnomad AMR exome

AF:

0.0144

Gnomad ASJ exome

AF:

0.0226

Gnomad EAS exome

AF:

0.00186

Gnomad SAS exome

AF:

0.0308

Gnomad FIN exome

AF:

0.00107

Gnomad NFE exome

AF:

0.00722

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.0138

AC:

19943

AN:

1450272

Hom.:

906

Cov.:

AF XY:

0.0136

AC XY:

9810

AN XY:

721800

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.0157

Gnomad4 ASJ exome

AF:

0.0209

Gnomad4 EAS exome

AF:

0.000989

Gnomad4 SAS exome

AF:

0.0300

Gnomad4 FIN exome

AF:

0.00111

Gnomad4 NFE exome

AF:

0.00718

Gnomad4 OTH exome

AF:

0.0212

GnomAD4 genome

AF:

0.0642

AC:

9764

AN:

152130

Hom.:

885

Cov.:

AF XY:

0.0629

AC XY:

4678

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.0269

Gnomad4 ASJ

AF:

0.0167

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0313

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00747

Gnomad4 OTH

AF:

0.0545

Alfa

AF:

0.0186

Hom.:

163

Bravo

AF:

0.0720

Asia WGS

AF:

0.0280

AC:

AN:

3474

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

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.5

DANN

Benign

0.49

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.

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