Genetic Variant ENSG00000271860:n.156-74498G>C (chr6-98024688-G-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000606913.5(ENSG00000271860):n.156-74498G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 169,920 control chromosomes in the GnomAD database, including 1,241 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 0.12 ( 1174 hom., cov: 32)

Exomes 𝑓: 0.092 ( 67 hom. )

Consequence

ENSG00000271860
ENST00000606913.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

6 publications found

Variant links:

COSMIC-nc: COSV71816442

Genes affected

ENSG00000271860 (HGNC:):

ENSG00000271860 links:

MIR2113 (HGNC:37058): (microRNA 2113) 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]

MIR2113 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR2113	NR_031579.1 link	n.*67G>C		downstream_gene_variant
MIR2113	unassigned_transcript_1157	n.*82G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000271860	ENST00000606913.5 link	n.156-74498G>C	intron_variant	Intron 1 of 4	5
ENSG00000271860	ENST00000607032.1 link	n.247-51379G>C	intron_variant	Intron 2 of 7	3
ENSG00000271860	ENST00000607823.5 link	n.267+55222G>C	intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18174

AN:

151874

Hom.:

1172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0921

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0867

Gnomad MID

AF:

0.0935

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.0923

AC:

1655

AN:

17926

Hom.:

AF XY:

0.0941

AC XY:

807

AN XY:

8576

show subpopulations

African (AFR)

AF:

0.0750

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.159

AC:

AN:

European-Finnish (FIN)

AF:

0.0906

AC:

1416

AN:

15628

Middle Eastern (MID)

AF:

0.0952

AC:

148

AN:

1554

European-Non Finnish (NFE)

AF:

0.140

AC:

AN:

272

Other (OTH)

AF:

0.102

AC:

AN:

284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

174

261

348

435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.120

AC:

18176

AN:

151994

Hom.:

1174

Cov.:

AF XY:

0.120

AC XY:

8903

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.0919

AC:

3810

AN:

41454

American (AMR)

AF:

0.188

AC:

2867

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

404

AN:

3466

East Asian (EAS)

AF:

0.189

AC:

972

AN:

5156

South Asian (SAS)

AF:

0.113

AC:

544

AN:

4822

European-Finnish (FIN)

AF:

0.0867

AC:

917

AN:

10576

Middle Eastern (MID)

AF:

0.0931

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.121

AC:

8225

AN:

67946

Other (OTH)

AF:

0.132

AC:

279

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

810

1620

2430

3240

4050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.0567

Hom.:

Bravo

AF:

0.129

Asia WGS

AF:

0.140

AC:

487

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

1.3

Splicing

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