rs1127348
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001384125.1(BLTP1):āc.15048T>Cā(p.His5016=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,609,210 control chromosomes in the GnomAD database, including 37,542 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.17 ( 2832 hom., cov: 32)
Exomes š: 0.21 ( 34710 hom. )
Consequence
BLTP1
NM_001384125.1 synonymous
NM_001384125.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.39
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 4-122359705-T-C is Benign according to our data. Variant chr4-122359705-T-C is described in ClinVar as [Benign]. Clinvar id is 1179225.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.39 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLTP1 | NM_001384125.1 | c.15048T>C | p.His5016= | synonymous_variant | 87/88 | ENST00000679879.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLTP1 | ENST00000679879.1 | c.15048T>C | p.His5016= | synonymous_variant | 87/88 | NM_001384125.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25275AN: 151962Hom.: 2834 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
25275
AN:
151962
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:
GnomAD3 exomes AF: 0.192 AC: 47580AN: 247316Hom.: 5518 AF XY: 0.195 AC XY: 26213AN XY: 134282
GnomAD3 exomes
AF:
AC:
47580
AN:
247316
Hom.:
AF XY:
AC XY:
26213
AN XY:
134282
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.210 AC: 305689AN: 1457130Hom.: 34710 Cov.: 30 AF XY: 0.209 AC XY: 151262AN XY: 725094
GnomAD4 exome
AF:
AC:
305689
AN:
1457130
Hom.:
Cov.:
30
AF XY:
AC XY:
151262
AN XY:
725094
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.166 AC: 25260AN: 152080Hom.: 2832 Cov.: 32 AF XY: 0.171 AC XY: 12706AN XY: 74342
GnomAD4 genome
?
AF:
AC:
25260
AN:
152080
Hom.:
Cov.:
32
AF XY:
AC XY:
12706
AN XY:
74342
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
382
AN:
3476
EpiCase
AF:
EpiControl
AF:
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 04, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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