rs12803915

Variant summary

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

The NR_030343.1(MIR612):​n.51G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 490,522 control chromosomes in the GnomAD database, including 7,664 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 0.17 ( 2285 hom., cov: 30)
Exomes 𝑓: 0.17 ( 5379 hom. )

Consequence

MIR612
NR_030343.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44
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=-0.74).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIR612NR_030343.1 linkuse as main transcriptn.51G>A non_coding_transcript_exon_variant 1/1
NEAT1NR_131012.1 linkuse as main transcriptn.21711G>A non_coding_transcript_exon_variant 1/1
MIR612unassigned_transcript_1908 use as main transcriptn.*11G>A downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR612ENST00000384994.1 linkuse as main transcriptn.51G>A non_coding_transcript_exon_variant 1/16
NEAT1ENST00000501122.2 linkuse as main transcriptn.21711G>A non_coding_transcript_exon_variant 1/16

Frequencies

GnomAD3 genomes
AF:
0.167
AC:
25323
AN:
151834
Hom.:
2283
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.334
Gnomad AMR
AF:
0.142
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.118
Gnomad MID
AF:
0.194
Gnomad NFE
AF:
0.209
Gnomad OTH
AF:
0.159
GnomAD3 exomes
AF:
0.164
AC:
29712
AN:
180892
Hom.:
2663
AF XY:
0.164
AC XY:
15893
AN XY:
96738
show subpopulations
Gnomad AFR exome
AF:
0.116
Gnomad AMR exome
AF:
0.130
Gnomad ASJ exome
AF:
0.193
Gnomad EAS exome
AF:
0.146
Gnomad SAS exome
AF:
0.118
Gnomad FIN exome
AF:
0.121
Gnomad NFE exome
AF:
0.207
Gnomad OTH exome
AF:
0.178
GnomAD4 exome
AF:
0.172
AC:
58085
AN:
338566
Hom.:
5379
Cov.:
0
AF XY:
0.169
AC XY:
32339
AN XY:
191724
show subpopulations
Gnomad4 AFR exome
AF:
0.125
Gnomad4 AMR exome
AF:
0.131
Gnomad4 ASJ exome
AF:
0.193
Gnomad4 EAS exome
AF:
0.142
Gnomad4 SAS exome
AF:
0.118
Gnomad4 FIN exome
AF:
0.124
Gnomad4 NFE exome
AF:
0.208
Gnomad4 OTH exome
AF:
0.181
GnomAD4 genome
AF:
0.167
AC:
25341
AN:
151956
Hom.:
2285
Cov.:
30
AF XY:
0.159
AC XY:
11838
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.142
Gnomad4 ASJ
AF:
0.193
Gnomad4 EAS
AF:
0.147
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.118
Gnomad4 NFE
AF:
0.209
Gnomad4 OTH
AF:
0.156
Alfa
AF:
0.193
Hom.:
1493
Bravo
AF:
0.170
Asia WGS
AF:
0.113
AC:
396
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
7.7
DANN
Benign
0.79
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.3

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: rs12803915; hg19: chr11-65211979; COSMIC: COSV66057836; API