GeneBe

ENST00000635687.1:n.387-393T>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000635687.1(MIR34AHG):​n.387-393T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,130 control chromosomes in the GnomAD database, including 41,952 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 0.74 ( 41952 hom., cov: 32)

Consequence

MIR34AHG
ENST00000635687.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.81

Publications

7 publications found
Variant links:
Genes affected
MIR34AHG (HGNC:51913): (MIR34A host gene)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR34AHGNR_132742.1 linkn.333-393T>G intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR34AHGENST00000635687.1 linkn.387-393T>G intron_variant Intron 1 of 1 1
MIR34AHGENST00000782879.1 linkn.464-12207T>G intron_variant Intron 2 of 2
MIR34AHGENST00000782880.1 linkn.339-12207T>G intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.741
AC:
112614
AN:
152012
Hom.:
41887
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.806
Gnomad AMI
AF:
0.727
Gnomad AMR
AF:
0.771
Gnomad ASJ
AF:
0.717
Gnomad EAS
AF:
0.751
Gnomad SAS
AF:
0.697
Gnomad FIN
AF:
0.670
Gnomad MID
AF:
0.718
Gnomad NFE
AF:
0.709
Gnomad OTH
AF:
0.733
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.741
AC:
112737
AN:
152130
Hom.:
41952
Cov.:
32
AF XY:
0.737
AC XY:
54777
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.807
AC:
33482
AN:
41496
American (AMR)
AF:
0.771
AC:
11789
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.717
AC:
2489
AN:
3470
East Asian (EAS)
AF:
0.752
AC:
3897
AN:
5180
South Asian (SAS)
AF:
0.696
AC:
3352
AN:
4814
European-Finnish (FIN)
AF:
0.670
AC:
7099
AN:
10592
Middle Eastern (MID)
AF:
0.718
AC:
211
AN:
294
European-Non Finnish (NFE)
AF:
0.709
AC:
48201
AN:
67978
Other (OTH)
AF:
0.736
AC:
1555
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1481
2963
4444
5926
7407
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
850
1700
2550
3400
4250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.651
Hom.:
2086
Bravo
AF:
0.753
Asia WGS
AF:
0.748
AC:
2604
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.51
DANN
Benign
0.42
PhyloP100
-2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs6577555; hg19: chr1-9212287; API