chr13-91354178-TTTAG-T

Variant names:

• chr13-91354178-TTTAG-T
• rs535569411
• ENST00000581816.2:n.4371_4374delTAGT

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP6 BS2

The ENST00000400282.8(MIR17HG):​n.532_535delTAGT 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 0.000637 in 152,302 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.00064 (0 hom., cov: 32)
• Consequence: MIR17HG ENST00000400282.8 non_coding_transcript_exon
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.67
• 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: Likely_benign. The variant received -5 ACMG points.

• BP6: Variant 13-91354178-TTTAG-T is Benign according to our data. Variant chr13-91354178-TTTAG-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3355368.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 97 AD,Unknown gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400282.8. 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.4371_4374delTAGT		non_coding_transcript_exon	Exon 3 of 3
	MIR17HG	NR_027349.2		n.665_668delTAGT		non_coding_transcript_exon	Exon 4 of 4
	MIR17HG	NR_027350.2		n.4756_4759delTAGT		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR17HG	ENST00000581816.2	TSL:1 MANE Select	n.4371_4374delTAGT		non_coding_transcript_exon	Exon 3 of 3
	MIR17HG	ENST00000400282.8	TSL:1	n.532_535delTAGT		non_coding_transcript_exon	Exon 4 of 4
	MIR17HG	ENST00000582141.7	TSL:1	n.4756_4759delTAGT		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.000637 AC: 97 AN: 152184 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

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: 0.000478

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

GnomAD4 genome AF: 0.000637 AC: 97 AN: 152302 Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44 AN XY: 74462

African (AFR) AF: 0.00229 AC: 95 AN: 41552

American (AMR) AF: 0.0000653 AC: 1 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68028

Other (OTH) AF: 0.000473 AC: 1 AN: 2114

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
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs535569411; hg19: chr13-92006432;