4-122212023-C-G

Position:

• chr4-122212023-C-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+928C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 976,296 control chromosomes in the GnomAD database, including 17,732 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 0.15 (2184 hom., cov: 32)
  • Exomes 𝑓: 0.19 (15548 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

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]

BLTP1 (HGNC:):

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 = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLTP1	NM_001384125.1	c.2247+928C>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+928C>G		intron_variant			NM_001384125.1	ENSP00000505357.1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22812 AN: 151828 Hom.: 2178 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.191 AC: 157427 AN: 824350 Hom.: 15548 Cov.: 18 AF XY: 0.191 AC XY: 72832 AN XY: 380940

Gnomad4 AFR exome AF: 0.0250

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.213

Gnomad4 EAS exome AF: 0.219

Gnomad4 SAS exome AF: 0.214

Gnomad4 FIN exome AF: 0.146

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.150 AC: 22834 AN: 151946 Hom.: 2184 Cov.: 32 AF XY: 0.150 AC XY: 11144 AN XY: 74274

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.181

Alfa AF: 0.0849 Hom.: 139

Bravo AF: 0.152

Asia WGS AF: 0.219 AC: 759 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	1.2
DANN	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6827444; hg19: chr4-123133178;