rs892583

Variant summary

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

The NR_147192.1(MIR4527HG):​n.38+104242G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,066 control chromosomes in the GnomAD database, including 45,925 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 0.77 ( 45925 hom., cov: 31)

Consequence

MIR4527HG
NR_147192.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.135
Variant links:
Genes affected
MIR4527HG (HGNC:31724): (MIR4527 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=-0.52).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIR4527HGNR_147192.1 linkuse as main transcriptn.38+104242G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR4527HGENST00000586905.3 linkuse as main transcriptn.37+104242G>A intron_variant, non_coding_transcript_variant 1
MIR4527HGENST00000598649.1 linkuse as main transcriptn.73+104206G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.774
AC:
117621
AN:
151948
Hom.:
45877
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.861
Gnomad AMI
AF:
0.849
Gnomad AMR
AF:
0.695
Gnomad ASJ
AF:
0.764
Gnomad EAS
AF:
0.891
Gnomad SAS
AF:
0.788
Gnomad FIN
AF:
0.811
Gnomad MID
AF:
0.718
Gnomad NFE
AF:
0.724
Gnomad OTH
AF:
0.750
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.774
AC:
117729
AN:
152066
Hom.:
45925
Cov.:
31
AF XY:
0.777
AC XY:
57722
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.861
Gnomad4 AMR
AF:
0.695
Gnomad4 ASJ
AF:
0.764
Gnomad4 EAS
AF:
0.891
Gnomad4 SAS
AF:
0.788
Gnomad4 FIN
AF:
0.811
Gnomad4 NFE
AF:
0.724
Gnomad4 OTH
AF:
0.753
Alfa
AF:
0.729
Hom.:
6583
Bravo
AF:
0.771
Asia WGS
AF:
0.818
AC:
2845
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.52
CADD
Benign
11
DANN
Benign
0.58

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: rs892583; hg19: chr18-44916374; API