4-122174548-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001384125.1(BLTP1):c.215-26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 1,602,402 control chromosomes in the GnomAD database, including 1,791 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.064 (885 hom., cov: 32)
  • Exomes 𝑓: 0.014 (906 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.486

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 4-122174548-C-T is Benign according to our data. Variant chr4-122174548-C-T is described in ClinVar as [Benign]. Clinvar id is 1231351.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP1	NM_001384125.1	c.215-26C>T		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.215-26C>T		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9739 AN: 152012 Hom.: 881 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00747

Gnomad OTH AF: 0.0551

GnomAD3 exomes AF: 0.0239 AC: 5760 AN: 240844 Hom.: 375 AF XY: 0.0208 AC XY: 2727 AN XY: 130868

Gnomad AFR exome AF: 0.213

Gnomad AMR exome AF: 0.0144

Gnomad ASJ exome AF: 0.0226

Gnomad EAS exome AF: 0.00186

Gnomad SAS exome AF: 0.0308

Gnomad FIN exome AF: 0.00107

Gnomad NFE exome AF: 0.00722

Gnomad OTH exome AF: 0.0155

GnomAD4 exome AF: 0.0138 AC: 19943 AN: 1450272 Hom.: 906 Cov.: 29 AF XY: 0.0136 AC XY: 9810 AN XY: 721800

Gnomad4 AFR exome AF: 0.210

Gnomad4 AMR exome AF: 0.0157

Gnomad4 ASJ exome AF: 0.0209

Gnomad4 EAS exome AF: 0.000989

Gnomad4 SAS exome AF: 0.0300

Gnomad4 FIN exome AF: 0.00111

Gnomad4 NFE exome AF: 0.00718

Gnomad4 OTH exome AF: 0.0212

GnomAD4 genome AF: 0.0642 AC: 9764 AN: 152130 Hom.: 885 Cov.: 32 AF XY: 0.0629 AC XY: 4678 AN XY: 74412

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.00747

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0186 Hom.: 163

Bravo AF: 0.0720

Asia WGS AF: 0.0280 AC: 98 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.5
Dann	Benign	0.49

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: rs10021037; hg19: chr4-123095703;