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GeneBe

rs10910099

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033467.4(MMEL1):c.1041+1771T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 150,834 control chromosomes in the GnomAD database, including 13,870 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 0.41 ( 13870 hom., cov: 32)

Consequence

MMEL1
NM_033467.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.116
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MMEL1NM_033467.4 linkuse as main transcriptc.1041+1771T>G intron_variant ENST00000378412.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MMEL1ENST00000378412.8 linkuse as main transcriptc.1041+1771T>G intron_variant 2 NM_033467.4 P1Q495T6-1
MMEL1ENST00000502556.5 linkuse as main transcriptc.570+1771T>G intron_variant 1 Q495T6-3
MMEL1ENST00000504800.5 linkuse as main transcriptc.1041+1771T>G intron_variant, NMD_transcript_variant 2 Q495T6-2

Frequencies

GnomAD3 genomes
AF:
0.412
AC:
62075
AN:
150714
Hom.:
13839
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.563
Gnomad AMI
AF:
0.153
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.304
Gnomad EAS
AF:
0.504
Gnomad SAS
AF:
0.504
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.322
Gnomad OTH
AF:
0.372
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.412
AC:
62154
AN:
150834
Hom.:
13870
Cov.:
32
AF XY:
0.416
AC XY:
30603
AN XY:
73584
show subpopulations
Gnomad4 AFR
AF:
0.563
Gnomad4 AMR
AF:
0.433
Gnomad4 ASJ
AF:
0.304
Gnomad4 EAS
AF:
0.503
Gnomad4 SAS
AF:
0.505
Gnomad4 FIN
AF:
0.356
Gnomad4 NFE
AF:
0.322
Gnomad4 OTH
AF:
0.378
Alfa
AF:
0.363
Hom.:
3681
Bravo
AF:
0.419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
1.9
Dann
Benign
0.36

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10910099; hg19: chr1-2533552; API