rs8002779

Variant names:

• chr13-91363723-G-A
• rs8002779
• ENST00000710414.1:n.5180G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710414.1(MIR17HG):​n.5180G>A 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 0.538 in 151,838 control chromosomes in the GnomAD database, including 22,588 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 0.54 (22588 hom., cov: 31)
• Consequence: MIR17HG ENST00000710414.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 23 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, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000710414.1	n.5180G>A		non_coding_transcript_exon_variant	Exon 2 of 2
MIR17HG	ENST00000710421.1	n.336+13953G>A		intron_variant	Intron 2 of 3
MIR17HG	ENST00000710422.1	n.407+13497G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81634 AN: 151720 Hom.: 22576 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.538 AC: 81670 AN: 151838 Hom.: 22588 Cov.: 31 AF XY: 0.536 AC XY: 39812 AN XY: 74220

African (AFR) AF: 0.415 AC: 17204 AN: 41418

American (AMR) AF: 0.621 AC: 9465 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1924 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2599 AN: 5164

South Asian (SAS) AF: 0.638 AC: 3072 AN: 4814

European-Finnish (FIN) AF: 0.486 AC: 5115 AN: 10514

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40340 AN: 67898

Other (OTH) AF: 0.564 AC: 1188 AN: 2108

Alfa AF: 0.576 Hom.: 88644

Bravo AF: 0.540

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.038
DANN	Benign	0.69
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs8002779; hg19: chr13-92015977;