Variant chr1-248826485-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The 1-248826485-T-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 154,760 control chromosomes in the GnomAD database, including 8,558 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 0.25 ( 8499 hom., cov: 32)

Exomes 𝑓: 0.19 ( 59 hom. )

Consequence

MIR3124
NR_036070.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.865

Variant links:

Genes affected

MIR3124 (HGNC:38262): (microRNA 3124) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR3124 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3124	NR_036070.1 linkuse as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3124	ENST00000582636.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37857

AN:

152024

Hom.:

8477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.572

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.0992

Gnomad EAS

AF:

0.534

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.0823

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0828

Gnomad OTH

AF:

0.202

GnomAD3 exomes

AF:

0.128

AC:

842

AN:

6578

Hom.:

118

AF XY:

0.104

AC XY:

332

AN XY:

3198

show subpopulations

Gnomad AFR exome

AF:

0.616

Gnomad AMR exome

AF:

0.246

Gnomad ASJ exome

AF:

0.0931

Gnomad EAS exome

AF:

0.600

Gnomad SAS exome

AF:

0.241

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0859

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.194

AC:

509

AN:

2618

Hom.:

Cov.:

AF XY:

0.186

AC XY:

251

AN XY:

1346

show subpopulations

Gnomad4 AFR exome

AF:

0.486

Gnomad4 AMR exome

AF:

0.750

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.0701

Gnomad4 NFE exome

AF:

0.0798

Gnomad4 OTH exome

AF:

0.345

GnomAD4 genome

AF:

0.249

AC:

37929

AN:

152142

Hom.:

8499

Cov.:

AF XY:

0.251

AC XY:

18656

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.572

Gnomad4 AMR

AF:

0.177

Gnomad4 ASJ

AF:

0.0992

Gnomad4 EAS

AF:

0.534

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.0823

Gnomad4 NFE

AF:

0.0828

Gnomad4 OTH

AF:

0.202

Alfa

AF:

0.146

Hom.:

2008

Bravo

AF:

0.273

Asia WGS

AF:

0.441

AC:

1528

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.8

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over