rs13119723

chr4-122297158-A-G

Variant summary

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

The NM_001384125.1(BLTP1):c.9389-4142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,240 control chromosomes in the GnomAD database, including 1,120 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 0.10 (1120 hom., cov: 33)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP1	NM_001384125.1	c.9389-4142A>G		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.9389-4142A>G		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15943 AN: 152122 Hom.: 1120 Cov.: 33

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.0984

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.105 AC: 15946 AN: 152240 Hom.: 1120 Cov.: 33 AF XY: 0.102 AC XY: 7560 AN XY: 74442

Gnomad4 AFR AF: 0.0282

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.0969

Alfa AF: 0.127 Hom.: 1334

Bravo AF: 0.0968

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.66
Dann	Benign	0.56

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: rs13119723; hg19: chr4-123218313;