chr13-91349218-A-G

Position:

• chr13-91349218-A-G

Variant summary

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

The NR_027350.1(MIR17HG):​n.141-480A>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 0.517 in 151,896 control chromosomes in the GnomAD database, including 21,348 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 0.52 (21348 hom., cov: 32)
• Consequence: MIR17HG NR_027350.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR17HG	NR_027350.1	n.141-480A>G		intron_variant, non_coding_transcript_variant
MIR17HG	NR_027349.1	n.141-480A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR17HG	ENST00000710422.1	n.264-480A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78456 AN: 151778 Hom.: 21339 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.517 AC: 78479 AN: 151896 Hom.: 21348 Cov.: 32 AF XY: 0.516 AC XY: 38314 AN XY: 74252

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.550

Alfa AF: 0.575 Hom.: 11657

Bravo AF: 0.517

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4284505; hg19: chr13-92001472; COSMIC: COSV63011082;