chr10-19620841-A-G

Variant names:

• chr10-19620841-A-G
• rs10827649
• NM_001142308.3:c.6137+4918A>G

Variant summary

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

The NM_001142308.3(MALRD1):​c.6137+4918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,704 control chromosomes in the GnomAD database, including 15,407 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 0.45 (15407 hom., cov: 31)
• Consequence: MALRD1 NM_001142308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142308.3. 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
	MALRD1	NM_001142308.3	MANE Select	c.6137+4918A>G		intron	N/A	NP_001135780.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALRD1	ENST00000454679.7	TSL:1 MANE Select	c.6137+4918A>G		intron	N/A	ENSP00000412763.3
	MALRD1	ENST00000377266.7	TSL:5	c.4207+12939A>G		intron	N/A	ENSP00000366477.3
	MALRD1	ENST00000377265.3	TSL:2	c.1187+4918A>G		intron	N/A	ENSP00000366476.3

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67965 AN: 151584 Hom.: 15376 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.449 AC: 68046 AN: 151704 Hom.: 15407 Cov.: 31 AF XY: 0.454 AC XY: 33660 AN XY: 74166

African (AFR) AF: 0.433 AC: 17925 AN: 41394

American (AMR) AF: 0.531 AC: 8072 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1931 AN: 3460

East Asian (EAS) AF: 0.461 AC: 2362 AN: 5120

South Asian (SAS) AF: 0.560 AC: 2701 AN: 4820

European-Finnish (FIN) AF: 0.420 AC: 4431 AN: 10546

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29063 AN: 67856

Other (OTH) AF: 0.465 AC: 976 AN: 2100

Alfa AF: 0.440 Hom.: 56924

Bravo AF: 0.458

Asia WGS AF: 0.492 AC: 1707 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.5
DANN	Benign	0.86
PhyloP100		0.26
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: rs10827649; hg19: chr10-19909770;