NM_001384125.1:c.6763-714A>C
Variant names:
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
NM_001384125.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.06
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 |
---|---|---|---|---|---|---|---|---|
BLTP1 | NM_001384125.1 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
BLTP1 | ENST00000679879.1 | c.6763-714A>C | intron_variant | Intron 42 of 87 | NM_001384125.1 | ENSP00000505357.1 |
Frequencies
GnomAD3 genomes AF: 0.126 AC: 19168AN: 151918Hom.: 1727 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
19168
AN:
151918
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0849 AC: 69642AN: 819998Hom.: 3354 AF XY: 0.0847 AC XY: 32097AN XY: 379120 show subpopulations
GnomAD4 exome
AF:
AC:
69642
AN:
819998
Hom.:
AF XY:
AC XY:
32097
AN XY:
379120
African (AFR)
AF:
AC:
4299
AN:
15512
American (AMR)
AF:
AC:
54
AN:
964
Ashkenazi Jewish (ASJ)
AF:
AC:
369
AN:
5066
East Asian (EAS)
AF:
AC:
11
AN:
3558
South Asian (SAS)
AF:
AC:
1053
AN:
16200
European-Finnish (FIN)
AF:
AC:
23
AN:
270
Middle Eastern (MID)
AF:
AC:
158
AN:
1588
European-Non Finnish (NFE)
AF:
AC:
61439
AN:
750004
Other (OTH)
AF:
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: 19194AN: 152036Hom.: 1736 Cov.: 32 AF XY: 0.125 AC XY: 9311AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
19194
AN:
152036
Hom.:
Cov.:
32
AF XY:
AC XY:
9311
AN XY:
74344
African (AFR)
AF:
AC:
10661
AN:
41430
American (AMR)
AF:
AC:
1096
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
217
AN:
3464
East Asian (EAS)
AF:
AC:
13
AN:
5176
South Asian (SAS)
AF:
AC:
311
AN:
4828
European-Finnish (FIN)
AF:
AC:
1014
AN:
10580
Middle Eastern (MID)
AF:
AC:
29
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5588
AN:
67982
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
152
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at