4-122170523-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.-33-92C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0671 in 1,335,392 control chromosomes in the GnomAD database, including 3,349 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.050 (269 hom., cov: 32)
  • Exomes 𝑓: 0.069 (3080 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.883

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=-0.9).
• BP6: Variant 4-122170523-C-T is Benign according to our data. Variant chr4-122170523-C-T is described in ClinVar as [Benign]. Clinvar id is 1278856.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP1	NM_001384125.1	c.-33-92C>T		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.-33-92C>T		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7598 AN: 151920 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0464

GnomAD4 exome AF: 0.0693 AC: 82034 AN: 1183354 Hom.: 3080 Cov.: 18 AF XY: 0.0686 AC XY: 39522 AN XY: 576078

Gnomad4 AFR exome AF: 0.0104

Gnomad4 AMR exome AF: 0.0419

Gnomad4 ASJ exome AF: 0.0461

Gnomad4 EAS exome AF: 0.000581

Gnomad4 SAS exome AF: 0.0345

Gnomad4 FIN exome AF: 0.0832

Gnomad4 NFE exome AF: 0.0752

Gnomad4 OTH exome AF: 0.0606

GnomAD4 genome AF: 0.0499 AC: 7589 AN: 152038 Hom.: 269 Cov.: 32 AF XY: 0.0505 AC XY: 3752 AN XY: 74300

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0659 Hom.: 70

Bravo AF: 0.0435

Asia WGS AF: 0.0140 AC: 50 AN: 3476

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 14, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.22
Dann	Benign	0.56

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: rs62323927; hg19: chr4-123091678;