Genetic Variant ENSG00000272180:n.82+36716A>T (chr2-55988955-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000606639.1(ENSG00000272180):n.82+36716A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 511,260 control chromosomes in the GnomAD database, including 1,351 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 0.084 ( 818 hom., cov: 32)

Exomes 𝑓: 0.047 ( 533 hom. )

Consequence

ENSG00000272180
ENST00000606639.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Publications

22 publications found

Variant links:

Genes affected

ENSG00000272180 (HGNC:):

ENSG00000272180 links:

MIR216A (HGNC:31593): (microRNA 216a) 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]

MIR216A links:

MIR217HG (HGNC:50537): (MIR217 host gene)

MIR217HG 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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR216A	NR_029629.1 link	n.105T>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR217HG	NR_126406.1 link	n.208+24654T>A	intron_variant	Intron 2 of 2
LOC105374690	XR_940109.3 link	n.587+36716A>T	intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000272180	ENST00000606639.1 link	n.82+36716A>T	intron_variant	Intron 1 of 6	1
MIR216A	ENST00000385063.1 link	n.105T>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR217HG	ENST00000446139.2 link	n.924+24654T>A	intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0844

AC:

12847

AN:

152126

Hom.:

818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.0756

Gnomad ASJ

AF:

0.0597

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0246

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0491

Gnomad OTH

AF:

0.0789

GnomAD2 exomes

AF:

0.0503

AC:

12450

AN:

247660

AF XY:

0.0486

show subpopulations

Gnomad AFR exome

AF:

0.184

Gnomad AMR exome

AF:

0.0433

Gnomad ASJ exome

AF:

0.0628

Gnomad EAS exome

AF:

0.000601

Gnomad FIN exome

AF:

0.0242

Gnomad NFE exome

AF:

0.0470

Gnomad OTH exome

AF:

0.0512

GnomAD4 exome

AF:

0.0465

AC:

16697

AN:

359016

Hom.:

533

Cov.:

AF XY:

0.0460

AC XY:

9257

AN XY:

201180

show subpopulations

African (AFR)

AF:

0.178

AC:

1816

AN:

10230

American (AMR)

AF:

0.0438

AC:

1555

AN:

35492

Ashkenazi Jewish (ASJ)

AF:

0.0608

AC:

695

AN:

11424

East Asian (EAS)

AF:

0.000636

AC:

AN:

12578

South Asian (SAS)

AF:

0.0429

AC:

2760

AN:

64324

European-Finnish (FIN)

AF:

0.0249

AC:

794

AN:

31886

Middle Eastern (MID)

AF:

0.0350

AC:

AN:

2774

European-Non Finnish (NFE)

AF:

0.0466

AC:

8142

AN:

174616

Other (OTH)

AF:

0.0529

AC:

830

AN:

15692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

675

1350

2025

2700

3375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

188

282

376

470

<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:

0.0845

AC:

12863

AN:

152244

Hom.:

818

Cov.:

AF XY:

0.0817

AC XY:

6083

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.180

AC:

7458

AN:

41508

American (AMR)

AF:

0.0757

AC:

1158

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0597

AC:

207

AN:

3470

East Asian (EAS)

AF:

0.00174

AC:

AN:

5184

South Asian (SAS)

AF:

0.0439

AC:

212

AN:

4830

European-Finnish (FIN)

AF:

0.0246

AC:

261

AN:

10614

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0491

AC:

3337

AN:

68018

Other (OTH)

AF:

0.0781

AC:

165

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

580

1159

1739

2318

2898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0421

Hom.:

Bravo

AF:

0.0909

Asia WGS

AF:

0.0310

AC:

106

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

1.4

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