rs1059276

Variant names:

• chr6-46839303-C-A
• rs1059276
• NM_005588.3:c.*167C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-46839303-C-A
• chr6-46839303-C-G

Variant summary

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

The NM_005588.3(MEP1A):​c.*167C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 540,010 control chromosomes in the GnomAD database, including 105,411 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 0.63 (30437 hom., cov: 29)
  • Exomes 𝑓: 0.62 (74974 hom.)
• Consequence: MEP1A NM_005588.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 5 publications found

Genes affected

MEP1A (HGNC:7015): (meprin A subunit alpha) Predicted to enable metalloendopeptidase activity. Predicted to be involved in proteolysis. Located in extracellular exosome. Part of meprin A complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005588.3. 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
	MEP1A	NM_005588.3	MANE Select	c.*167C>A		3_prime_UTR	Exon 14 of 14	NP_005579.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEP1A	ENST00000230588.9	TSL:1 MANE Select	c.*167C>A		3_prime_UTR	Exon 14 of 14	ENSP00000230588.4
	MEP1A	ENST00000879644.1		c.*167C>A		3_prime_UTR	Exon 15 of 15	ENSP00000549703.1
	MEP1A	ENST00000879647.1		c.*167C>A		3_prime_UTR	Exon 14 of 14	ENSP00000549706.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95366 AN: 151074 Hom.: 30398 Cov.: 29

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.618 AC: 240101 AN: 388820 Hom.: 74974 Cov.: 5 AF XY: 0.622 AC XY: 125221 AN XY: 201370

African (AFR) AF: 0.583 AC: 6529 AN: 11198

American (AMR) AF: 0.724 AC: 10400 AN: 14370

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 8333 AN: 12022

East Asian (EAS) AF: 0.542 AC: 15299 AN: 28212

South Asian (SAS) AF: 0.684 AC: 19606 AN: 28676

European-Finnish (FIN) AF: 0.579 AC: 16074 AN: 27762

Middle Eastern (MID) AF: 0.670 AC: 1161 AN: 1734

European-Non Finnish (NFE) AF: 0.612 AC: 148119 AN: 241850

Other (OTH) AF: 0.634 AC: 14580 AN: 22996

GnomAD4 genome AF: 0.631 AC: 95455 AN: 151190 Hom.: 30437 Cov.: 29 AF XY: 0.629 AC XY: 46455 AN XY: 73800

African (AFR) AF: 0.599 AC: 24636 AN: 41136

American (AMR) AF: 0.714 AC: 10821 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2392 AN: 3466

East Asian (EAS) AF: 0.564 AC: 2895 AN: 5136

South Asian (SAS) AF: 0.730 AC: 3453 AN: 4732

European-Finnish (FIN) AF: 0.576 AC: 6013 AN: 10436

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43088 AN: 67828

Other (OTH) AF: 0.639 AC: 1336 AN: 2092

Alfa AF: 0.519 Hom.: 1497

Bravo AF: 0.637

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		0.13
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: rs1059276; hg19: chr6-46807040;