rs7699742

Variant names:

• chr4-122343330-T-C
• rs7699742
• NM_001384125.1:c.12617-80T>C

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.12617-80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,551,920 control chromosomes in the GnomAD database, including 89,729 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.29 (7533 hom., cov: 32)
  • Exomes 𝑓: 0.33 (82196 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.456

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=-0.83).
• BP6: Variant 4-122343330-T-C is Benign according to our data. Variant chr4-122343330-T-C is described in ClinVar as [Benign]. Clinvar id is 1222692.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLTP1	NM_001384125.1	c.12617-80T>C		intron_variant	Intron 74 of 87	ENST00000679879.1	NP_001371054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLTP1	ENST00000679879.1	c.12617-80T>C		intron_variant	Intron 74 of 87		NM_001384125.1	ENSP00000505357.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44254 AN: 152016 Hom.: 7533 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.335 AC: 468436 AN: 1399786 Hom.: 82196 Cov.: 28 AF XY: 0.332 AC XY: 229365 AN XY: 691398

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.490

Gnomad4 ASJ exome AF: 0.221

Gnomad4 EAS exome AF: 0.469

Gnomad4 SAS exome AF: 0.271

Gnomad4 FIN exome AF: 0.470

Gnomad4 NFE exome AF: 0.335

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.291 AC: 44259 AN: 152134 Hom.: 7533 Cov.: 32 AF XY: 0.298 AC XY: 22149 AN XY: 74356

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.274

Alfa AF: 0.323 Hom.: 4676

Bravo AF: 0.281

Asia WGS AF: 0.297 AC: 1030 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 12, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
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: rs7699742; hg19: chr4-123264485; COSMIC: COSV52691055;