chr4-122172862-C-T

Variant names:

• chr4-122172862-C-T
• rs72923986
• NM_001384125.1:c.98-174C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001384125.1(BLTP1):​c.98-174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00857 in 915,164 control chromosomes in the GnomAD database, including 492 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.036 (340 hom., cov: 32)
  • Exomes 𝑓: 0.0031 (152 hom.)
• Consequence: BLTP1 NM_001384125.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

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]

BLTP1 Gene-Disease associations (from GenCC):

• Alkuraya-Kucinskas syndrome

  Inheritance: AR Classification: STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 4-122172862-C-T is Benign according to our data. Variant chr4-122172862-C-T is described in ClinVar as Benign. ClinVar VariationId is 1235578.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384125.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLTP1	NM_001384125.1	MANE Select	c.98-174C>T		intron	N/A	NP_001371054.1	A0A7P0T938
	BLTP1	NM_015312.4		c.98-174C>T		intron	N/A	NP_056127.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLTP1	ENST00000679879.1	MANE Select	c.98-174C>T		intron	N/A	ENSP00000505357.1	A0A7P0T938
	BLTP1	ENST00000388738.8	TSL:1	c.98-174C>T		intron	N/A	ENSP00000373390.4	A0A8J8Z0T9
	BLTP1	ENST00000264501.8	TSL:5	c.98-174C>T		intron	N/A	ENSP00000264501.4	Q2LD37-1

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5442 AN: 152098 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000441

Gnomad OTH AF: 0.0263

GnomAD4 exome AF: 0.00313 AC: 2385 AN: 762948 Hom.: 152 AF XY: 0.00297 AC XY: 1053 AN XY: 354056

African (AFR) AF: 0.141 AC: 2032 AN: 14408

American (AMR) AF: 0.00644 AC: 6 AN: 932

Ashkenazi Jewish (ASJ) AF: 0.00705 AC: 33 AN: 4684

East Asian (EAS) AF: 0.00 AC: 0 AN: 3284

South Asian (SAS) AF: 0.000332 AC: 5 AN: 15066

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 248

Middle Eastern (MID) AF: 0.00678 AC: 10 AN: 1474

European-Non Finnish (NFE) AF: 0.000192 AC: 134 AN: 698026

Other (OTH) AF: 0.00665 AC: 165 AN: 24826

GnomAD4 genome AF: 0.0359 AC: 5462 AN: 152216 Hom.: 340 Cov.: 32 AF XY: 0.0349 AC XY: 2596 AN XY: 74442

African (AFR) AF: 0.125 AC: 5171 AN: 41506

American (AMR) AF: 0.0127 AC: 194 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000441 AC: 30 AN: 68010

Other (OTH) AF: 0.0260 AC: 55 AN: 2114

Alfa AF: 0.0175 Hom.: 14

Bravo AF: 0.0407

Asia WGS AF: 0.00665 AC: 24 AN: 3472

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.023
DANN	Benign	0.47
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs72923986; hg19: chr4-123094017;