NM_033467.4:c.536-230G>A

Variant names:

• chr1-2607299-C-T
• rs12138909
• NM_033467.4:c.536-230G>A

Variant summary

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

The NM_033467.4(MMEL1):​c.536-230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,216 control chromosomes in the GnomAD database, including 1,166 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 0.10 (1166 hom., cov: 33)
• Consequence: MMEL1 NM_033467.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.77
• Publications: 11 publications found

Genes affected

MMEL1 (HGNC:14668): (membrane metalloendopeptidase like 1) The protein encoded by this gene is a member of the neutral endopeptidase (NEP) or membrane metallo-endopeptidase (MME) family. Family members play important roles in pain perception, arterial pressure regulation, phosphate metabolism and homeostasis. This protein is a type II transmembrane protein and is thought to be expressed as a secreted protein. This gene is expressed mainly in testis with weak expression in the brain, kidney, and heart. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMEL1	NM_033467.4	c.536-230G>A		intron_variant	Intron 6 of 23	ENST00000378412.8	NP_258428.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMEL1	ENST00000378412.8	c.536-230G>A		intron_variant	Intron 6 of 23	2	NM_033467.4	ENSP00000367668.3
MMEL1	ENST00000502556.5	c.480+2095G>A		intron_variant	Intron 5 of 18	1		ENSP00000422492.1
MMEL1	ENST00000504800.5	n.536-230G>A		intron_variant	Intron 5 of 22	2		ENSP00000425477.1
MMEL1	ENST00000509374.1	n.365-230G>A		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15964 AN: 152098 Hom.: 1166 Cov.: 33

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00329

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.105 AC: 15966 AN: 152216 Hom.: 1166 Cov.: 33 AF XY: 0.103 AC XY: 7652 AN XY: 74406

African (AFR) AF: 0.0274 AC: 1140 AN: 41566

American (AMR) AF: 0.102 AC: 1556 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5162

South Asian (SAS) AF: 0.0846 AC: 408 AN: 4822

European-Finnish (FIN) AF: 0.166 AC: 1756 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10377 AN: 67986

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.134 Hom.: 2267

Bravo AF: 0.0969

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.58
PhyloP100		-3.8
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: rs12138909; hg19: chr1-2538738;