rs767649

Variant summary

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

The NR_001458.3(MIR155HG):​n.199-1483T>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 0.0799 in 151,960 control chromosomes in the GnomAD database, including 826 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 0.080 ( 826 hom., cov: 32)

Consequence

MIR155HG
NR_001458.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.127
Variant links:
Genes affected
MIR155HG (HGNC:35460): (MIR155 host gene) This gene represents a microRNA host gene. The long RNA transcribed from this gene is expressed at high levels in lymphoma and may function as an oncogene. [provided by RefSeq, Dec 2017]

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=-0.67).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIR155HGNR_001458.3 linkuse as main transcriptn.199-1483T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR155HGENST00000456917.2 linkuse as main transcriptn.424-1483T>A intron_variant, non_coding_transcript_variant 5
MIR155HGENST00000659862.2 linkuse as main transcriptn.296-1483T>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0800
AC:
12149
AN:
151842
Hom.:
828
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0472
Gnomad AMI
AF:
0.0537
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.0329
Gnomad EAS
AF:
0.367
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.0816
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0682
Gnomad OTH
AF:
0.0768
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0799
AC:
12149
AN:
151960
Hom.:
826
Cov.:
32
AF XY:
0.0838
AC XY:
6222
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.0471
Gnomad4 AMR
AF:
0.110
Gnomad4 ASJ
AF:
0.0329
Gnomad4 EAS
AF:
0.368
Gnomad4 SAS
AF:
0.164
Gnomad4 FIN
AF:
0.0816
Gnomad4 NFE
AF:
0.0681
Gnomad4 OTH
AF:
0.0760
Alfa
AF:
0.0675
Hom.:
56
Bravo
AF:
0.0801
Asia WGS
AF:
0.254
AC:
874
AN:
3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
12
DANN
Benign
0.84

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: rs767649; hg19: chr21-26944722; API