4-1297325-G-T

Variant summary

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

The NM_001017405.3(MAEA):​c.69+7343G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,174 control chromosomes in the GnomAD database, including 12,011 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 0.36 ( 12011 hom., cov: 33)

Consequence

MAEA
NM_001017405.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77
Variant links:
Genes affected
MAEA (HGNC:13731): (macrophage erythroblast attacher, E3 ubiquitin ligase) This gene encodes a protein that mediates the attachment of erythroblasts to macrophages. This attachment promotes terminal maturation and enucleation of erythroblasts, presumably by suppressing apoptosis. The encoded protein is an integral membrane protein with the N-terminus on the extracellular side and the C-terminus on the cytoplasmic side of the cell. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAEANM_001017405.3 linkc.69+7343G>T intron_variant Intron 1 of 8 ENST00000303400.9 NP_001017405.1 Q7L5Y9-1B3KRN7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAEAENST00000303400.9 linkc.69+7343G>T intron_variant Intron 1 of 8 1 NM_001017405.3 ENSP00000302830.4 Q7L5Y9-1

Frequencies

GnomAD3 genomes
AF:
0.363
AC:
55220
AN:
152056
Hom.:
12009
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.135
Gnomad AMI
AF:
0.524
Gnomad AMR
AF:
0.347
Gnomad ASJ
AF:
0.435
Gnomad EAS
AF:
0.0932
Gnomad SAS
AF:
0.358
Gnomad FIN
AF:
0.537
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.494
Gnomad OTH
AF:
0.343
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.363
AC:
55223
AN:
152174
Hom.:
12011
Cov.:
33
AF XY:
0.361
AC XY:
26856
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.135
Gnomad4 AMR
AF:
0.347
Gnomad4 ASJ
AF:
0.435
Gnomad4 EAS
AF:
0.0931
Gnomad4 SAS
AF:
0.360
Gnomad4 FIN
AF:
0.537
Gnomad4 NFE
AF:
0.494
Gnomad4 OTH
AF:
0.338
Alfa
AF:
0.442
Hom.:
4417
Bravo
AF:
0.335
Asia WGS
AF:
0.219
AC:
765
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
6.2
DANN
Benign
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs13108904; hg19: chr4-1291113; API