rs6534347

Positions:

• chr4-122277280-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.8591+1258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,064 control chromosomes in the GnomAD database, including 29,942 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 0.62 (29942 hom., cov: 31)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP1	NM_001384125.1	c.8591+1258A>G		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.8591+1258A>G		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94781 AN: 151946 Hom.: 29911 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.624 AC: 94871 AN: 152064 Hom.: 29942 Cov.: 31 AF XY: 0.619 AC XY: 45978 AN XY: 74330

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.660

Alfa AF: 0.623 Hom.: 3688

Bravo AF: 0.626

Asia WGS AF: 0.576 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.51

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: rs6534347; hg19: chr4-123198435;