rs4773624

Positions:

• chr13-91367475-G-A

Variant summary

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

The ENST00000710421.1(MIR17HG):​n.336+17705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,912 control chromosomes in the GnomAD database, including 26,486 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 0.59 (26486 hom., cov: 31)
• Consequence: MIR17HG ENST00000710421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000710421.1	n.336+17705G>A		intron_variant
MIR17HG	ENST00000710422.1	n.407+17249G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89228 AN: 151794 Hom.: 26466 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.588 AC: 89297 AN: 151912 Hom.: 26486 Cov.: 31 AF XY: 0.584 AC XY: 43389 AN XY: 74236

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.608

Alfa AF: 0.614 Hom.: 27792

Bravo AF: 0.593

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4773624; hg19: chr13-92019729;