dbSNP rs7336610: MIR17HG:n.3074C>T (chr13-91352883-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000581816.2(MIR17HG):n.3074C>T 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 0.472 in 151,662 control chromosomes in the GnomAD database, including 18,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.47 ( 18387 hom., cov: 29)

Consequence

MIR17HG
ENST00000581816.2 non_coding_transcript_exon

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.480

Publications

21 publications found

Variant links:

Genes affected

MIR17HG (HGNC:23564): (miR-17-92a-1 cluster host gene) This gene is the host gene for the MIR17-92 cluster, a group of at least six microRNAs (miRNAs) that may be involved in cell survival, proliferation, differentiation, and angiogenesis. Amplification of this gene has been found in several lymphomas and solid tumors. Two non-protein coding transcript variants have been found for this host gene, but only the longest is a polycistronic transcript containing the MIR17-92 cluster. [provided by RefSeq, May 2012]

MIR17HG Gene-Disease associations (from GenCC):

Feingold syndrome type 2
Inheritance: AD, Unknown Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

MIR17HG links:

ENSG00000292285 (HGNC:):

ENSG00000292285 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 13-91352883-C-T is Benign according to our data. Variant chr13-91352883-C-T is described in ClinVar as Benign. ClinVar VariationId is 3060743.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581816.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR17HG	NR_197388.1	MANE Select	n.3074C>T	non_coding_transcript_exon	Exon 3 of 3
MIR17HG	NR_027350.2		n.3459C>T	non_coding_transcript_exon	Exon 2 of 2
MIR17HG	NR_027349.2		n.418-1050C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR17HG	ENST00000581816.2	TSL:1 MANE Select	n.3074C>T	non_coding_transcript_exon	Exon 3 of 3
MIR17HG	ENST00000582141.7	TSL:1	n.3459C>T	non_coding_transcript_exon	Exon 2 of 2
MIR17HG	ENST00000400282.8	TSL:1	n.285-1050C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71506

AN:

151546

Hom.:

18375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.587

Gnomad ASJ

AF:

0.525

Gnomad EAS

AF:

0.501

Gnomad SAS

AF:

0.586

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.515

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.472

AC:

71523

AN:

151662

Hom.:

18387

Cov.:

AF XY:

0.472

AC XY:

34937

AN XY:

74086

show subpopulations

African (AFR)

AF:

0.258

AC:

10677

AN:

41324

American (AMR)

AF:

0.587

AC:

8949

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.525

AC:

1820

AN:

3466

East Asian (EAS)

AF:

0.501

AC:

2572

AN:

5138

South Asian (SAS)

AF:

0.586

AC:

2805

AN:

4788

European-Finnish (FIN)

AF:

0.448

AC:

4694

AN:

10478

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.562

AC:

38182

AN:

67918

Other (OTH)

AF:

0.515

AC:

1084

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1751

3502

5253

7004

8755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<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:

0.496

Hom.:

2451

Bravo

AF:

0.473

Asia WGS

AF:

0.495

AC:

1721

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

MIR17HG-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.56

PhyloP100

-0.48

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over