rs7319045

Positions:

• chr13-91372320-A-G
• chr13-91372320-A-T

Variant summary

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

The ENST00000710422.1(MIR17HG):​n.407+22094A>G 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 0.553 in 151,994 control chromosomes in the GnomAD database, including 23,991 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 0.55 (23991 hom., cov: 33)
• Consequence: MIR17HG ENST00000710422.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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 = 0.637 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	ENST00000710422.1	n.407+22094A>G		intron_variant, non_coding_transcript_variant
MIR17HG	ENST00000710421.1	n.336+22550A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84099 AN: 151876 Hom.: 23987 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.553 AC: 84123 AN: 151994 Hom.: 23991 Cov.: 33 AF XY: 0.552 AC XY: 40973 AN XY: 74280

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.583

Alfa AF: 0.603 Hom.: 22402

Bravo AF: 0.555

Asia WGS AF: 0.534 AC: 1852 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7319045; hg19: chr13-92024574;