rs4505848

Positions:

• chr4-122211337-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.2247+242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 150,584 control chromosomes in the GnomAD database, including 7,527 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 0.29 (7527 hom., cov: 32)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLTP1	NM_001384125.1	c.2247+242A>G		intron_variant		ENST00000679879.1	NP_001371054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLTP1	ENST00000679879.1	c.2247+242A>G		intron_variant			NM_001384125.1	ENSP00000505357	A2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44239 AN: 150468 Hom.: 7527 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.294 AC: 44246 AN: 150584 Hom.: 7527 Cov.: 32 AF XY: 0.301 AC XY: 22142 AN XY: 73592

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.278

Alfa AF: 0.330 Hom.: 13603

Bravo AF: 0.280

Asia WGS AF: 0.300 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.72

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: rs4505848; hg19: chr4-123132492;