rs8002779

chr13-91363723-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710422.1(MIR17HG):n.407+13497G>A variant causes a intron, non coding transcript 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 ENST00000710422.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR17HG	ENST00000710422.1	n.407+13497G>A		intron_variant, non_coding_transcript_variant
MIR17HG	ENST00000710414.1	n.5180G>A		non_coding_transcript_exon_variant	2/2
MIR17HG	ENST00000710421.1	n.336+13953G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.564

Alfa AF: 0.586 Hom.: 60902

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8002779; hg19: chr13-92015977;