GeneBe

rs4027132

Positions:

Variant summary

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

The variant allele was found at a frequency of 0.577 in 150,690 control chromosomes in the GnomAD database, including 25,137 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 0.58 ( 25137 hom., cov: 30)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.11897366G>A intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR3681HGENST00000438292.5 linkuse as main transcriptn.31+31451G>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.577
AC:
86898
AN:
150586
Hom.:
25106
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.609
Gnomad AMI
AF:
0.603
Gnomad AMR
AF:
0.594
Gnomad ASJ
AF:
0.546
Gnomad EAS
AF:
0.435
Gnomad SAS
AF:
0.569
Gnomad FIN
AF:
0.674
Gnomad MID
AF:
0.633
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.568
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.577
AC:
86973
AN:
150690
Hom.:
25137
Cov.:
30
AF XY:
0.583
AC XY:
42801
AN XY:
73436
show subpopulations
Gnomad4 AFR
AF:
0.609
Gnomad4 AMR
AF:
0.594
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.435
Gnomad4 SAS
AF:
0.569
Gnomad4 FIN
AF:
0.674
Gnomad4 NFE
AF:
0.552
Gnomad4 OTH
AF:
0.570
Alfa
AF:
0.545
Hom.:
41371
Bravo
AF:
0.567
Asia WGS
AF:
0.465
AC:
1617
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.6
DANN
Benign
0.51

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: rs4027132; hg19: chr2-12037492; API