Genetic Variant BLTP1:c.627+95G>A (chr4-122187607-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001384125.1(BLTP1):c.627+95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 1,286,140 control chromosomes in the GnomAD database, including 634,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.96 ( 70996 hom., cov: 31)

Exomes 𝑓: 1.0 ( 563492 hom. )

Consequence

BLTP1
NM_001384125.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.981

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 was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 4-122187607-G-A is Benign according to our data. Variant chr4-122187607-G-A is described in ClinVar as [Benign]. Clinvar id is 1252960.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLTP1	NM_001384125.1 link	c.627+95G>A		intron_variant	Intron 8 of 87	ENST00000679879.1	NP_001371054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLTP1	ENST00000679879.1 link	c.627+95G>A		intron_variant	Intron 8 of 87		NM_001384125.1	ENSP00000505357.1		A0A7P0T938

Frequencies

GnomAD3 genomes

AF:

0.965

AC:

146578

AN:

151934

Hom.:

70945

Cov.:

show subpopulations

Gnomad AFR

AF:

0.877

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.988

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.994

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.976

GnomAD4 exome

AF:

0.997

AC:

1130308

AN:

1134088

Hom.:

563492

AF XY:

0.997

AC XY:

567300

AN XY:

568954

show subpopulations

African (AFR)

AF:

0.874

AC:

21052

AN:

24088

American (AMR)

AF:

0.992

AC:

25002

AN:

25208

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

20290

AN:

20292

East Asian (EAS)

AF:

1.00

AC:

35572

AN:

35572

South Asian (SAS)

AF:

1.00

AC:

60453

AN:

60472

European-Finnish (FIN)

AF:

1.00

AC:

48780

AN:

48780

Middle Eastern (MID)

AF:

0.996

AC:

3873

AN:

3890

European-Non Finnish (NFE)

AF:

1.00

AC:

867679

AN:

867842

Other (OTH)

AF:

0.993

AC:

47607

AN:

47944

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

157

315

472

630

787

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.965

AC:

146689

AN:

152052

Hom.:

70996

Cov.:

AF XY:

0.966

AC XY:

71782

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.877

AC:

36407

AN:

41492

American (AMR)

AF:

0.988

AC:

15070

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

3468

AN:

3468

East Asian (EAS)

AF:

1.00

AC:

5185

AN:

5186

South Asian (SAS)

AF:

1.00

AC:

4819

AN:

4820

European-Finnish (FIN)

AF:

1.00

AC:

10600

AN:

10600

Middle Eastern (MID)

AF:

0.993

AC:

292

AN:

294

European-Non Finnish (NFE)

AF:

0.999

AC:

67877

AN:

67912

Other (OTH)

AF:

0.976

AC:

2059

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

251

502

752

1003

1254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.975

Hom.:

18794

Bravo

AF:

0.960

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 12, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

6.4

(source)

DANN

Benign

0.38

PhyloP100

0.98

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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4-122187607-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over