Genetic Variant ENSG00000309922:n.157T>G (chr1-248826485-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000845987.1(ENSG00000309922):n.157T>G 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 0.248 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

ENSG00000309922
ENST00000845987.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.865

Publications

14 publications found

Variant links:

Genes affected

ENSG00000309922 (HGNC:):

ENSG00000309922 links:

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 was made for transcript

Our verdict: Benign. The variant received -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	Effect
MIR3124	NR_036070.1 link	n.*42T>G	downstream_gene_variant
MIR3124	unassigned_transcript_318	n.*82T>G	downstream_gene_variant
MIR3124	unassigned_transcript_319	n.*46T>G	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309922	ENST00000845987.1 link	n.157T>G		non_coding_transcript_exon_variant	Exon 1 of 1
MIR3124	ENST00000582636.1 link	n.*42T>G		downstream_gene_variant		6

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

GnomAD2 exomes

AF:

0.128

AC:

842

AN:

6578

AF XY:

0.104

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 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

African (AFR)

AF:

0.486

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.196

AC:

AN:

European-Finnish (FIN)

AF:

0.0701

AC:

AN:

428

Middle Eastern (MID)

AF:

0.207

AC:

337

AN:

1630

European-Non Finnish (NFE)

AF:

0.0798

AC:

AN:

188

Other (OTH)

AF:

0.345

AC:

AN:

194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.249

AC:

37929

AN:

152142

Hom.:

8499

Cov.:

AF XY:

0.251

AC XY:

18656

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.572

AC:

23728

AN:

41450

American (AMR)

AF:

0.177

AC:

2712

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0992

AC:

344

AN:

3468

East Asian (EAS)

AF:

0.534

AC:

2759

AN:

5170

South Asian (SAS)

AF:

0.289

AC:

1392

AN:

4824

European-Finnish (FIN)

AF:

0.0823

AC:

874

AN:

10624

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0828

AC:

5631

AN:

68000

Other (OTH)

AF:

0.202

AC:

426

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1097

2194

3291

4388

5485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.194

Hom.:

5955

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

(source)

DANN

Benign

0.72

PhyloP100

-0.86

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over