rs9589207

Positions:

• chr13-91351335-G-A
• chr13-91351335-G-C

Variant summary

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

The ENST00000581816.1(MIR17HG):​n.1271G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00802 in 531,700 control chromosomes in the GnomAD database, including 156 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 0.021 (131 hom., cov: 33)
  • Exomes 𝑓: 0.0028 (25 hom.)
• Consequence: MIR17HG ENST00000581816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

Genes affected

MIR17HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.07 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR17HG	NR_027350.1	n.1778G>A		non_coding_transcript_exon_variant	2/2
MIR92A1	NR_029508.1	n.22G>A		non_coding_transcript_exon_variant	1/1
MIR92A1	unassigned_transcript_2148	n.12G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000581816.1	n.1271G>A		non_coding_transcript_exon_variant	3/3	1
MIR17HG	ENST00000582141.6	n.1778G>A		non_coding_transcript_exon_variant	2/2	1
MIR17HG	ENST00000400282.7	n.284+1109G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0210 AC: 3198 AN: 152162 Hom.: 130 Cov.: 33

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.0158

GnomAD3 exomes AF: 0.00544 AC: 1367 AN: 251074 Hom.: 41 AF XY: 0.00375 AC XY: 510 AN XY: 135910

Gnomad AFR exome AF: 0.0734

Gnomad AMR exome AF: 0.00350

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000229

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000291

Gnomad OTH exome AF: 0.00277

GnomAD4 exome AF: 0.00278 AC: 1053 AN: 379420 Hom.: 25 Cov.: 0 AF XY: 0.00210 AC XY: 453 AN XY: 215446

Gnomad4 AFR exome AF: 0.0732

Gnomad4 AMR exome AF: 0.00356

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000375

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000195

Gnomad4 OTH exome AF: 0.00519

GnomAD4 genome AF: 0.0211 AC: 3209 AN: 152280 Hom.: 131 Cov.: 33 AF XY: 0.0200 AC XY: 1487 AN XY: 74474

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.0105

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.00583 Hom.: 47

Bravo AF: 0.0235

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9589207; hg19: chr13-92003589;