rs4288027

chr4-122262050-A-Cchr4-122262050-A-Gchr4-122262050-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BLTP1	NM_001384125.1	c.6763-714A>C		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.6763-714A>C		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19168 AN: 151918 Hom.: 1727 Cov.: 32

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

Gnomad4 AFR exome AF: 0.277

Gnomad4 AMR exome AF: 0.0560

Gnomad4 ASJ exome AF: 0.0728

Gnomad4 EAS exome AF: 0.00309

Gnomad4 SAS exome AF: 0.0650

Gnomad4 FIN exome AF: 0.0852

Gnomad4 NFE exome AF: 0.0819

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.126 AC: 19194 AN: 152036 Hom.: 1736 Cov.: 32 AF XY: 0.125 AC XY: 9311 AN XY: 74344

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.0626

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0644

Gnomad4 FIN AF: 0.0958

Gnomad4 NFE AF: 0.0822

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0773 Hom.: 378

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

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

Other links and lift over

dbSNP: rs4288027; hg19: chr4-123183205;