NM_001384125.1:c.6763-714A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001384125.1(BLTP1):​c.6763-714A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 972,034 control chromosomes in the GnomAD database, including 5,090 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 0.13 ( 1736 hom., cov: 32)
Exomes 𝑓: 0.085 ( 3354 hom. )

Consequence

BLTP1
NM_001384125.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06
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]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BLTP1NM_001384125.1 linkc.6763-714A>C intron_variant Intron 42 of 87 ENST00000679879.1 NP_001371054.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BLTP1ENST00000679879.1 linkc.6763-714A>C intron_variant Intron 42 of 87 NM_001384125.1 ENSP00000505357.1 A0A7P0T938

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19168
AN:
151918
Hom.:
1727
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.257
Gnomad AMI
AF:
0.0408
Gnomad AMR
AF:
0.0719
Gnomad ASJ
AF:
0.0626
Gnomad EAS
AF:
0.00251
Gnomad SAS
AF:
0.0650
Gnomad FIN
AF:
0.0958
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0822
Gnomad OTH
AF:
0.110
GnomAD4 exome
AF:
0.0849
AC:
69642
AN:
819998
Hom.:
3354
AF XY:
0.0847
AC XY:
32097
AN XY:
379120
show subpopulations
African (AFR)
AF:
0.277
AC:
4299
AN:
15512
American (AMR)
AF:
0.0560
AC:
54
AN:
964
Ashkenazi Jewish (ASJ)
AF:
0.0728
AC:
369
AN:
5066
East Asian (EAS)
AF:
0.00309
AC:
11
AN:
3558
South Asian (SAS)
AF:
0.0650
AC:
1053
AN:
16200
European-Finnish (FIN)
AF:
0.0852
AC:
23
AN:
270
Middle Eastern (MID)
AF:
0.0995
AC:
158
AN:
1588
European-Non Finnish (NFE)
AF:
0.0819
AC:
61439
AN:
750004
Other (OTH)
AF:
0.0833
AC:
2236
AN:
26836
Heterozygous variant carriers
0
3002
6005
9007
12010
15012
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
3164
6328
9492
12656
15820
<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:
0.126
AC:
19194
AN:
152036
Hom.:
1736
Cov.:
32
AF XY:
0.125
AC XY:
9311
AN XY:
74344
show subpopulations
African (AFR)
AF:
0.257
AC:
10661
AN:
41430
American (AMR)
AF:
0.0718
AC:
1096
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.0626
AC:
217
AN:
3464
East Asian (EAS)
AF:
0.00251
AC:
13
AN:
5176
South Asian (SAS)
AF:
0.0644
AC:
311
AN:
4828
European-Finnish (FIN)
AF:
0.0958
AC:
1014
AN:
10580
Middle Eastern (MID)
AF:
0.0986
AC:
29
AN:
294
European-Non Finnish (NFE)
AF:
0.0822
AC:
5588
AN:
67982
Other (OTH)
AF:
0.108
AC:
228
AN:
2108
Heterozygous variant carriers
0
804
1608
2411
3215
4019
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
196
392
588
784
980
<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:
0.0830
Hom.:
484
Bravo
AF:
0.129
Asia WGS
AF:
0.0440
AC:
152
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.41
DANN
Benign
0.65
Mutation Taster
=100/0
polymorphism (auto)

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.

Other links and lift over

dbSNP: rs4288027; hg19: chr4-123183205; API