rs2274658

Variant names:

• chr6-46833334-G-A
• NM_005588.3:c.1405G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-46833334-G-A
• chr6-46833334-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005588.3(MEP1A):​c.1405G>A​(p.Val469Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V469L) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: MEP1A NM_005588.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03330025).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEP1A	NM_005588.3	c.1405G>A	p.Val469Ile	missense_variant	Exon 11 of 14	ENST00000230588.9	NP_005579.2
MEP1A	XM_011514628.2	c.1489G>A	p.Val497Ile	missense_variant	Exon 10 of 13		XP_011512930.1
MEP1A	XM_011514629.3	c.1405G>A	p.Val469Ile	missense_variant	Exon 11 of 14		XP_011512931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEP1A	ENST00000230588.9	c.1405G>A	p.Val469Ile	missense_variant	Exon 11 of 14	1	NM_005588.3	ENSP00000230588.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461884 Hom.: 0 Cov.: 45 AF XY: 0.00000138 AC XY: 1 AN XY: 727244

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.29
DANN	Benign	0.20
DEOGEN2	Benign	0.096	T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.079	N
LIST_S2	Benign	0.67	T;T
M_CAP	Benign	0.0076	T
MetaRNN	Benign	0.033	T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.81	L;.
PrimateAI	Benign	0.35	T
PROVEAN	Benign	0.010	N;.
REVEL	Benign	0.022
Sift	Benign	1.0	T;.
Sift4G	Benign	1.0	T;T
Polyphen		0.016	B;B
Vest4		0.036
MutPred		0.36		Loss of catalytic residue at V469 (P = 0.0922);.;
MVP		0.095
MPC		0.088
ClinPred		0.040	T
GERP RS		1.2
Varity_R		0.018
gMVP		0.052

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-46801071;