rs149052230

Variant names:

• chr13-91353079-C-T
• rs149052230
• ENST00000581816.2:n.3270C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS2

The ENST00000581816.2(MIR17HG):​n.3270C>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 0.000654 in 137,588 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.00065 (0 hom., cov: 26)
• Consequence: MIR17HG ENST00000581816.2 non_coding_transcript_exon
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.659
• Publications: 0 publications found

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)

ENSG00000292285 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 13-91353079-C-T is Benign according to our data. Variant chr13-91353079-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3029756.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 90 AD,Unknown gene.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR17HG	NR_197388.1	MANE Select	n.3270C>T		non_coding_transcript_exon	Exon 3 of 3
	MIR17HG	NR_027350.2		n.3655C>T		non_coding_transcript_exon	Exon 2 of 2
	MIR17HG	NR_027349.2		n.418-854C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR17HG	ENST00000581816.2	TSL:1 MANE Select	n.3270C>T		non_coding_transcript_exon	Exon 3 of 3
	MIR17HG	ENST00000582141.7	TSL:1	n.3655C>T		non_coding_transcript_exon	Exon 2 of 2
	MIR17HG	ENST00000400282.8	TSL:1	n.285-854C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000655 AC: 90 AN: 137508 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.00244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000805

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000552

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

GnomAD4 genome AF: 0.000654 AC: 90 AN: 137588 Hom.: 0 Cov.: 26 AF XY: 0.000658 AC XY: 43 AN XY: 65322

African (AFR) AF: 0.00243 AC: 88 AN: 36168

American (AMR) AF: 0.0000804 AC: 1 AN: 12444

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3426

East Asian (EAS) AF: 0.00 AC: 0 AN: 4718

South Asian (SAS) AF: 0.00 AC: 0 AN: 4430

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7306

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 226

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66138

Other (OTH) AF: 0.000547 AC: 1 AN: 1828

Alfa AF: 0.000569 Hom.: 0

Bravo AF: 0.000710

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	MIR17HG-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.50
PhyloP100		-0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs149052230; hg19: chr13-92005333;