4-122175683-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.294-167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 155,292 control chromosomes in the GnomAD database, including 885 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.064 (884 hom., cov: 32)
  • Exomes 𝑓: 0.011 (1 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.375

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=-1.01).
• BP6: Variant 4-122175683-C-T is Benign according to our data. Variant chr4-122175683-C-T is described in ClinVar as [Benign]. Clinvar id is 1294831.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.294-167C>T		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.294-167C>T		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9741 AN: 152012 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0272

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: 0.0550

GnomAD4 exome AF: 0.0114 AC: 36 AN: 3162 Hom.: 1 AF XY: 0.0105 AC XY: 16 AN XY: 1530

Gnomad4 AFR exome AF: 0.156

Gnomad4 ASJ exome AF: 0.0455

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0536

Gnomad4 NFE exome AF: 0.00687

Gnomad4 OTH exome AF: 0.0217

GnomAD4 genome AF: 0.0642 AC: 9766 AN: 152130 Hom.: 884 Cov.: 32 AF XY: 0.0628 AC XY: 4671 AN XY: 74378

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0271

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: 0.0325 Hom.: 71

Bravo AF: 0.0720

Asia WGS AF: 0.0280 AC: 98 AN: 3470

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	-1.0
Cadd	Benign	0.24
Dann	Benign	0.47

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: rs28602944; hg19: chr4-123096838;