chr10-19640584-T-C

Variant names:

• chr10-19640584-T-C
• rs1326986
• NM_001142308.3:c.6137+24661T>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.6137+24661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 152,312 control chromosomes in the GnomAD database, including 204 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 0.041 (204 hom., cov: 32)
• Consequence: MALRD1 NM_001142308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0572 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALRD1	NM_001142308.3	MANE Select	c.6137+24661T>C		intron	N/A	NP_001135780.2	Q5VYJ5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALRD1	ENST00000454679.7	TSL:1 MANE Select	c.6137+24661T>C		intron	N/A	ENSP00000412763.3	Q5VYJ5
	MALRD1	ENST00000377266.7	TSL:5	c.4207+32682T>C		intron	N/A	ENSP00000366477.3	U5GXS0
	MALRD1	ENST00000377265.3	TSL:2	c.1187+24661T>C		intron	N/A	ENSP00000366476.3	H0Y3D6

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6241 AN: 152194 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0410 AC: 6245 AN: 152312 Hom.: 204 Cov.: 32 AF XY: 0.0406 AC XY: 3025 AN XY: 74478

African (AFR) AF: 0.0113 AC: 469 AN: 41580

American (AMR) AF: 0.0394 AC: 602 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0641 AC: 222 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4828

European-Finnish (FIN) AF: 0.0459 AC: 487 AN: 10614

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3994 AN: 68018

Other (OTH) AF: 0.0492 AC: 104 AN: 2114

Alfa AF: 0.0261 Hom.: 146

Bravo AF: 0.0380

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism

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: rs1326986; hg19: chr10-19929513;