chr4-99574660-T-A

Variant names:

• chr4-99574660-T-A
• rs1800804
• NM_000253.4:c.-101-149T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000253.4(MTTP):​c.-101-149T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTTP NM_000253.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 24 publications found

Genes affected

MTTP (HGNC:7467): (microsomal triglyceride transfer protein) MTP encodes the large subunit of the heterodimeric microsomal triglyceride transfer protein. Protein disulfide isomerase (PDI) completes the heterodimeric microsomal triglyceride transfer protein, which has been shown to play a central role in lipoprotein assembly. Mutations in MTP can cause abetalipoproteinemia. [provided by RefSeq, Jul 2008]

MTTP Gene-Disease associations (from GenCC):

• abetalipoproteinemia

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, PanelApp Australia, G2P

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000253.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTTP	NM_000253.4		c.-101-149T>A		intron	N/A	NP_000244.2
	MTTP	NM_001300785.2		c.-188-7245T>A		intron	N/A	NP_001287714.2
	MTTP	NM_001386140.1	MANE Select	c.-250T>A		upstream_gene	N/A	NP_001373069.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTTP	ENST00000457717.6	TSL:5	c.-101-149T>A		intron	N/A	ENSP00000400821.1
	MTTP	ENST00000511045.6	TSL:2	c.-188-7245T>A		intron	N/A	ENSP00000427679.2
	MTTP	ENST00000511610.6	TSL:4	c.-101-149T>A		intron	N/A	ENSP00000422178.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 605412 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 318842

African (AFR) AF: 0.00 AC: 0 AN: 15354

American (AMR) AF: 0.00 AC: 0 AN: 26582

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16780

East Asian (EAS) AF: 0.00 AC: 0 AN: 29018

South Asian (SAS) AF: 0.00 AC: 0 AN: 56832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28388

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2996

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 398726

Other (OTH) AF: 0.00 AC: 0 AN: 30736

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 7468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.13
DANN	Benign	0.54
PhyloP100		-0.77
PromoterAI		-0.10	Neutral

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: rs1800804; hg19: chr4-100495817;