16-14315801-G-A

Variant summary

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

The ENST00000570945.2(MIR193BHG):​n.293-10212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,208 control chromosomes in the GnomAD database, including 40,827 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 0.72 ( 40827 hom., cov: 33)

Consequence

MIR193BHG
ENST00000570945.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

Publications

2 publications found
Variant links:
Genes affected
MIR193BHG (HGNC:51945): (MIR193b-365a 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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR193BHGNR_132983.2 linkn.355-10212G>A intron_variant Intron 1 of 1
MIR193BHGNR_132984.2 linkn.294-10212G>A intron_variant Intron 1 of 1
MIR193BHGNR_170633.1 linkn.152-10212G>A intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR193BHGENST00000570945.2 linkn.293-10212G>A intron_variant Intron 1 of 1 3
MIR193BHGENST00000634265.3 linkn.419-10212G>A intron_variant Intron 1 of 1 5
MIR193BHGENST00000641175.1 linkn.122-10212G>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.720
AC:
109508
AN:
152090
Hom.:
40768
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.919
Gnomad AMI
AF:
0.574
Gnomad AMR
AF:
0.651
Gnomad ASJ
AF:
0.643
Gnomad EAS
AF:
0.765
Gnomad SAS
AF:
0.690
Gnomad FIN
AF:
0.626
Gnomad MID
AF:
0.734
Gnomad NFE
AF:
0.633
Gnomad OTH
AF:
0.723
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.720
AC:
109629
AN:
152208
Hom.:
40827
Cov.:
33
AF XY:
0.720
AC XY:
53557
AN XY:
74396
show subpopulations
African (AFR)
AF:
0.919
AC:
38200
AN:
41578
American (AMR)
AF:
0.650
AC:
9942
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.643
AC:
2230
AN:
3468
East Asian (EAS)
AF:
0.765
AC:
3963
AN:
5182
South Asian (SAS)
AF:
0.690
AC:
3327
AN:
4822
European-Finnish (FIN)
AF:
0.626
AC:
6619
AN:
10566
Middle Eastern (MID)
AF:
0.741
AC:
218
AN:
294
European-Non Finnish (NFE)
AF:
0.634
AC:
43074
AN:
67992
Other (OTH)
AF:
0.727
AC:
1534
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1524
3048
4571
6095
7619
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
820
1640
2460
3280
4100
<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:
0.689
Hom.:
12980
Bravo
AF:
0.727
Asia WGS
AF:
0.751
AC:
2612
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.12
DANN
Benign
0.56
PhyloP100
-1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs30222; hg19: chr16-14409658; API