rs7657746

chr4-122240464-A-G

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.4671+111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 859,802 control chromosomes in the GnomAD database, including 23,991 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.24 (4778 hom., cov: 32)
  • Exomes 𝑓: 0.22 (19213 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0280

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 4-122240464-A-G is Benign according to our data. Variant chr4-122240464-A-G is described in ClinVar as [Benign]. Clinvar id is 1244401.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP1	NM_001384125.1	c.4671+111A>G		intron_variant		ENST00000679879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP1	ENST00000679879.1	c.4671+111A>G		intron_variant			NM_001384125.1	A2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36504 AN: 152028 Hom.: 4781 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.220 AC: 155918 AN: 707656 Hom.: 19213 AF XY: 0.217 AC XY: 79273 AN XY: 364758

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.237

Gnomad4 EAS exome AF: 0.0354

Gnomad4 SAS exome AF: 0.133

Gnomad4 FIN exome AF: 0.136

Gnomad4 NFE exome AF: 0.246

Gnomad4 OTH exome AF: 0.225

GnomAD4 genome AF: 0.240 AC: 36514 AN: 152146 Hom.: 4778 Cov.: 32 AF XY: 0.230 AC XY: 17094 AN XY: 74386

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.247

Alfa AF: 0.238 Hom.: 708

Bravo AF: 0.249

Asia WGS AF: 0.116 AC: 404 AN: 3478

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.67

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: rs7657746; hg19: chr4-123161619;