2-60358671-T-C

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.920+599A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,068 control chromosomes in the GnomAD database, including 16,542 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 0.46 ( 16542 hom., cov: 32)

Consequence

MIR4432HG
ENST00000441598.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411
Variant links:
Genes affected
MIR4432HG (HGNC:52005): (MIR4432 host gene)

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=-0.73).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR4432HGENST00000441598.2 linkn.920+599A>G intron_variant Intron 4 of 7 3

Frequencies

GnomAD3 genomes
AF:
0.463
AC:
70406
AN:
151950
Hom.:
16538
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.399
Gnomad AMI
AF:
0.387
Gnomad AMR
AF:
0.553
Gnomad ASJ
AF:
0.541
Gnomad EAS
AF:
0.669
Gnomad SAS
AF:
0.506
Gnomad FIN
AF:
0.436
Gnomad MID
AF:
0.566
Gnomad NFE
AF:
0.463
Gnomad OTH
AF:
0.511
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.463
AC:
70431
AN:
152068
Hom.:
16542
Cov.:
32
AF XY:
0.465
AC XY:
34572
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.399
Gnomad4 AMR
AF:
0.553
Gnomad4 ASJ
AF:
0.541
Gnomad4 EAS
AF:
0.669
Gnomad4 SAS
AF:
0.507
Gnomad4 FIN
AF:
0.436
Gnomad4 NFE
AF:
0.463
Gnomad4 OTH
AF:
0.509
Alfa
AF:
0.474
Hom.:
2766
Bravo
AF:
0.471
Asia WGS
AF:
0.536
AC:
1865
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
6.4
DANN
Benign
0.64

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: rs243019; hg19: chr2-60585806; API