rs7319045

Variant names:

• chr13-91372320-A-G
• rs7319045
• ENST00000710421.1:n.336+22550A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000710421.1(MIR17HG):​n.336+22550A>G variant causes a intron 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 ENST00000710421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 42 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 = 0.637 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	ENST00000710421.1	n.336+22550A>G		intron_variant	Intron 2 of 3
MIR17HG	ENST00000710422.1	n.407+22094A>G		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.418 AC: 17326 AN: 41456

American (AMR) AF: 0.623 AC: 9507 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2604 AN: 5174

South Asian (SAS) AF: 0.656 AC: 3168 AN: 4826

European-Finnish (FIN) AF: 0.515 AC: 5438 AN: 10566

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42008 AN: 67934

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.594 Hom.: 74255

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7319045; hg19: chr13-92024574;