rs4773624

Variant names:

• chr13-91367475-G-A
• rs4773624
• ENST00000710421.1:n.336+17705G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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: Unknown, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710421.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR17HG	ENST00000710421.1		n.336+17705G>A		intron	N/A
	MIR17HG	ENST00000710422.1		n.407+17249G>A		intron	N/A

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

African (AFR) AF: 0.537 AC: 22217 AN: 41390

American (AMR) AF: 0.638 AC: 9739 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2581 AN: 5148

South Asian (SAS) AF: 0.657 AC: 3162 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5436 AN: 10558

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.619 AC: 42039 AN: 67960

Other (OTH) AF: 0.608 AC: 1281 AN: 2106

Alfa AF: 0.610 Hom.: 36185

Bravo AF: 0.593

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.61
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4773624; hg19: chr13-92019729;