4-122194347-A-G

Position:

• chr4-122194347-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.1052+1968A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 161,474 control chromosomes in the GnomAD database, including 1,260 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 0.11 (1110 hom., cov: 32)
  • Exomes 𝑓: 0.17 (150 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLTP1	NM_001384125.1	c.1052+1968A>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.1052+1968A>G		intron_variant			NM_001384125.1	ENSP00000505357.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16208 AN: 152154 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0974

GnomAD4 exome AF: 0.167 AC: 1536 AN: 9202 Hom.: 150 AF XY: 0.167 AC XY: 750 AN XY: 4502

Gnomad4 AFR exome AF: 0.0313

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.116

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.173

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.106 AC: 16210 AN: 152272 Hom.: 1110 Cov.: 32 AF XY: 0.103 AC XY: 7654 AN XY: 74464

Gnomad4 AFR AF: 0.0404

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.145 Hom.: 3540

Bravo AF: 0.0989

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.43

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: rs13151961; hg19: chr4-123115502;