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GeneBe

rs10495594

Positions:

Variant summary

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

The NR_110196.1(MIR3681HG):​n.327+23418G>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 0.113 in 151,904 control chromosomes in the GnomAD database, including 1,831 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 0.11 ( 1831 hom., cov: 31)

Consequence

MIR3681HG
NR_110196.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.358
Variant links:
Genes affected
MIR3681HG (HGNC:52001): (MIR3681 host gene)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIR3681HGNR_110196.1 linkuse as main transcriptn.327+23418G>A intron_variant, non_coding_transcript_variant
LOC105373432XR_922806.2 linkuse as main transcriptn.368-479C>T intron_variant, non_coding_transcript_variant
LOC105373432XR_922807.2 linkuse as main transcriptn.279-479C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR3681HGENST00000412294.5 linkuse as main transcriptn.315+23418G>A intron_variant, non_coding_transcript_variant 2
ENST00000701120.1 linkuse as main transcriptn.390-479C>T intron_variant, non_coding_transcript_variant
MIR3681HGENST00000438292.5 linkuse as main transcriptn.246+23418G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.113
AC:
17158
AN:
151786
Hom.:
1823
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0421
Gnomad AMI
AF:
0.0285
Gnomad AMR
AF:
0.234
Gnomad ASJ
AF:
0.0648
Gnomad EAS
AF:
0.459
Gnomad SAS
AF:
0.400
Gnomad FIN
AF:
0.0807
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0909
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.113
AC:
17191
AN:
151904
Hom.:
1831
Cov.:
31
AF XY:
0.123
AC XY:
9169
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.0424
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.0648
Gnomad4 EAS
AF:
0.460
Gnomad4 SAS
AF:
0.399
Gnomad4 FIN
AF:
0.0807
Gnomad4 NFE
AF:
0.0909
Gnomad4 OTH
AF:
0.126
Alfa
AF:
0.111
Hom.:
687
Bravo
AF:
0.119
Asia WGS
AF:
0.418
AC:
1452
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
11
DANN
Benign
0.57

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: rs10495594; hg19: chr2-12330399; API