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rs1127348

chr4-122359705-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001384125.1(BLTP1):c.15048T>C(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 (★).

Frequency

Genomes: 𝑓 0.17 ( 2832 hom., cov: 32)
Exomes 𝑓: 0.21 ( 34710 hom. )

Consequence

BLTP1
NM_001384125.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.39
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 made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=2.39 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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
BLTP1NM_001384125.1 linkuse as main transcriptc.15048T>C p.His5016= synonymous_variant 87/88 ENST00000679879.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BLTP1ENST00000679879.1 linkuse as main transcriptc.15048T>C p.His5016= synonymous_variant 87/88 NM_001384125.1 A2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.166
AC:
25275
AN:
151962
Hom.:
2834
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0388
Gnomad AMI
AF:
0.169
Gnomad AMR
AF:
0.131
Gnomad ASJ
AF:
0.184
Gnomad EAS
AF:
0.134
Gnomad SAS
AF:
0.132
Gnomad FIN
AF:
0.365
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.160
GnomAD3 exomes
AF:
0.192
AC:
47580
AN:
247316
Hom.:
5518
AF XY:
0.195
AC XY:
26213
AN XY:
134282
show subpopulations
Gnomad AFR exome
AF:
0.0329
Gnomad AMR exome
AF:
0.0991
Gnomad ASJ exome
AF:
0.184
Gnomad EAS exome
AF:
0.136
Gnomad SAS exome
AF:
0.143
Gnomad FIN exome
AF:
0.365
Gnomad NFE exome
AF:
0.233
Gnomad OTH exome
AF:
0.199
GnomAD4 exome
AF:
0.210
AC:
305689
AN:
1457130
Hom.:
34710
Cov.:
30
AF XY:
0.209
AC XY:
151262
AN XY:
725094
show subpopulations
Gnomad4 AFR exome
AF:
0.0320
Gnomad4 AMR exome
AF:
0.103
Gnomad4 ASJ exome
AF:
0.187
Gnomad4 EAS exome
AF:
0.123
Gnomad4 SAS exome
AF:
0.141
Gnomad4 FIN exome
AF:
0.358
Gnomad4 NFE exome
AF:
0.223
Gnomad4 OTH exome
AF:
0.187
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.166
AC:
25260
AN:
152080
Hom.:
2832
Cov.:
32
AF XY:
0.171
AC XY:
12706
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.0387
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.184
Gnomad4 EAS
AF:
0.134
Gnomad4 SAS
AF:
0.131
Gnomad4 FIN
AF:
0.365
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.160
Alfa
AF:
0.212
Hom.:
8003
Bravo
AF:
0.144
Asia WGS
AF:
0.110
AC:
382
AN:
3476
EpiCase
AF:
0.214
EpiControl
AF:
0.214

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 submitterclinical testingGeneDxMay 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
4.7
Dann
Benign
0.66

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: rs1127348; hg19: chr4-123280860; COSMIC: COSV52662755; API