NM_001142308.3:c.4846-24218T>C

Variant names:

• chr10-19426089-T-C
• rs9888035
• NM_001142308.3:c.4846-24218T>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.4846-24218T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,160 control chromosomes in the GnomAD database, including 4,008 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 0.18 (4008 hom., cov: 32)
• Consequence: MALRD1 NM_001142308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 1 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]

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 (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MALRD1	NM_001142308.3	c.4846-24218T>C		intron_variant	Intron 28 of 39	ENST00000454679.7	NP_001135780.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MALRD1	ENST00000454679.7	c.4846-24218T>C		intron_variant	Intron 28 of 39	1	NM_001142308.3	ENSP00000412763.3
MALRD1	ENST00000377266.7	c.2952+36480T>C		intron_variant	Intron 15 of 24	5		ENSP00000366477.3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27905 AN: 152042 Hom.: 3982 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.184 AC: 27989 AN: 152160 Hom.: 4008 Cov.: 32 AF XY: 0.178 AC XY: 13215 AN XY: 74424

African (AFR) AF: 0.399 AC: 16555 AN: 41450

American (AMR) AF: 0.123 AC: 1883 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3470

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5180

South Asian (SAS) AF: 0.0675 AC: 326 AN: 4828

European-Finnish (FIN) AF: 0.0476 AC: 505 AN: 10614

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.112 AC: 7598 AN: 68012

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.147 Hom.: 369

Bravo AF: 0.202

Asia WGS AF: 0.0810 AC: 280 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.66
PhyloP100		0.43
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: rs9888035; hg19: chr10-19715018;