GeneBe

rs7302017

Positions:

Variant summary

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

The ENST00000550290.2(MIRLET7IHG):​n.85-2802G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,136 control chromosomes in the GnomAD database, including 48,611 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 0.80 ( 48611 hom., cov: 32)

Consequence

MIRLET7IHG
ENST00000550290.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.59
Variant links:
Genes affected

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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIRLET7IHGNR_186001.1 linkuse as main transcriptn.94-2802G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIRLET7IHGENST00000550290.2 linkuse as main transcriptn.85-2802G>A intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.795
AC:
120860
AN:
152018
Hom.:
48567
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.757
Gnomad AMI
AF:
0.834
Gnomad AMR
AF:
0.675
Gnomad ASJ
AF:
0.908
Gnomad EAS
AF:
0.595
Gnomad SAS
AF:
0.733
Gnomad FIN
AF:
0.851
Gnomad MID
AF:
0.877
Gnomad NFE
AF:
0.849
Gnomad OTH
AF:
0.807
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.795
AC:
120958
AN:
152136
Hom.:
48611
Cov.:
32
AF XY:
0.790
AC XY:
58732
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.757
Gnomad4 AMR
AF:
0.675
Gnomad4 ASJ
AF:
0.908
Gnomad4 EAS
AF:
0.594
Gnomad4 SAS
AF:
0.734
Gnomad4 FIN
AF:
0.851
Gnomad4 NFE
AF:
0.849
Gnomad4 OTH
AF:
0.805
Alfa
AF:
0.833
Hom.:
65641
Bravo
AF:
0.780
Asia WGS
AF:
0.670
AC:
2332
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
0.26
DANN
Benign
0.53

Splicing

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: rs7302017; hg19: chr12-63004583; API