5-132367886-G-C

Variant summary

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

The ENST00000621103.4(MIR3936HG):​n.74-1105C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,116 control chromosomes in the GnomAD database, including 7,279 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 0.30 ( 7279 hom., cov: 33)

Consequence

MIR3936HG
ENST00000621103.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

Publications

29 publications found
Variant links:
Genes affected
MIR3936HG (HGNC:40538): (MIR3936 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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR3936HGNR_110997.1 linkn.74-1105C>G intron_variant Intron 1 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR3936HGENST00000621103.4 linkn.74-1105C>G intron_variant Intron 1 of 7 1
MIR3936HGENST00000457998.2 linkn.233-1105C>G intron_variant Intron 1 of 1 2
MIR3936HGENST00000649993.1 linkn.244-1105C>G intron_variant Intron 1 of 4

Frequencies

GnomAD3 genomes
AF:
0.298
AC:
45349
AN:
151998
Hom.:
7275
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.206
Gnomad AMI
AF:
0.131
Gnomad AMR
AF:
0.293
Gnomad ASJ
AF:
0.307
Gnomad EAS
AF:
0.381
Gnomad SAS
AF:
0.568
Gnomad FIN
AF:
0.429
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.295
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.298
AC:
45381
AN:
152116
Hom.:
7279
Cov.:
33
AF XY:
0.310
AC XY:
23059
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.206
AC:
8539
AN:
41508
American (AMR)
AF:
0.293
AC:
4482
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.307
AC:
1066
AN:
3470
East Asian (EAS)
AF:
0.382
AC:
1977
AN:
5182
South Asian (SAS)
AF:
0.569
AC:
2740
AN:
4816
European-Finnish (FIN)
AF:
0.429
AC:
4512
AN:
10526
Middle Eastern (MID)
AF:
0.398
AC:
117
AN:
294
European-Non Finnish (NFE)
AF:
0.312
AC:
21205
AN:
68006
Other (OTH)
AF:
0.295
AC:
624
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1613
3227
4840
6454
8067
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
464
928
1392
1856
2320
<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:
0.214
Hom.:
563
Bravo
AF:
0.277
Asia WGS
AF:
0.477
AC:
1653
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.3
DANN
Benign
0.64
PhyloP100
0.10

Splicing

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

Publications

Other links and lift over

dbSNP: rs2631372; hg19: chr5-131703578; API