10-19615941-ATTT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001142308.3(MALRD1):c.6137+27_6137+29del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,459,676 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
MALRD1
NM_001142308.3 intron
NM_001142308.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.565
Genes affected
MALRD1 (HGNC:24331): (MAM and LDL receptor class A domain containing 1) This gene encodes a conserved protein that features multiple MAM (meprin-A5-protein tyrosine phosphatase mu) and LDLR A2 (low density lipoprotein receptor A2) domains. Expression of this gene is enriched in the small intestine and is upregulated during differentiation of a human cell line that exhibits properties of intestinal epithelial cells. The encoded protein has been shown to modulate production of FGF19 in a human intestinal cell line and may regulate bile acid metabolism in the liver. A synergistic interaction between an allele of this gene and the APOE E4 allele is associated with an elevated risk of Alzheimer's disease in human patients. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 10-19615941-ATTT-A is Benign according to our data. Variant chr10-19615941-ATTT-A is described in ClinVar as [Benign]. Clinvar id is 2776137.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MALRD1 | NM_001142308.3 | c.6137+27_6137+29del | intron_variant | ENST00000454679.7 | NP_001135780.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MALRD1 | ENST00000454679.7 | c.6137+27_6137+29del | intron_variant | 1 | NM_001142308.3 | ENSP00000412763 | P1 | |||
MALRD1 | ENST00000377265.3 | c.1188+27_1188+29del | intron_variant | 2 | ENSP00000366476 | |||||
MALRD1 | ENST00000377266.7 | c.4207+8048_4207+8050del | intron_variant | 5 | ENSP00000366477 |
Frequencies
GnomAD3 genomes AF: 0.0000200 AC: 3AN: 149896Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0000188 AC: 2AN: 106568Hom.: 0 AF XY: 0.0000174 AC XY: 1AN XY: 57586
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GnomAD4 exome AF: 0.0000130 AC: 17AN: 1309780Hom.: 0 AF XY: 0.0000108 AC XY: 7AN XY: 645534
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GnomAD4 genome AF: 0.0000200 AC: 3AN: 149896Hom.: 0 Cov.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 73066
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 12, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at