10-19571889-A-C

Variant names:

• chr10-19571889-A-C
• rs17729837
• NM_001142308.3:c.5680+4186A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142308.3(MALRD1):​c.5680+4186A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,982 control chromosomes in the GnomAD database, including 11,815 homozygotes. 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: 𝑓 0.37 (11815 hom., cov: 32)
• Consequence: MALRD1 NM_001142308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 3 publications found

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]

ENSG00000306612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MALRD1	NM_001142308.3	c.5680+4186A>C		intron_variant	Intron 33 of 39	ENST00000454679.7	NP_001135780.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MALRD1	ENST00000454679.7	c.5680+4186A>C		intron_variant	Intron 33 of 39	1	NM_001142308.3	ENSP00000412763.3

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56616 AN: 151866 Hom.: 11820 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.359

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.373 AC: 56617 AN: 151982 Hom.: 11815 Cov.: 32 AF XY: 0.372 AC XY: 27588 AN XY: 74254

African (AFR) AF: 0.177 AC: 7335 AN: 41500

American (AMR) AF: 0.354 AC: 5401 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1904 AN: 5160

South Asian (SAS) AF: 0.312 AC: 1500 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5425 AN: 10540

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32520 AN: 67924

Other (OTH) AF: 0.358 AC: 757 AN: 2114

Alfa AF: 0.415 Hom.: 1873

Bravo AF: 0.350

Asia WGS AF: 0.360 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.68
PhyloP100		-0.23
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: rs17729837; hg19: chr10-19860818;