rs7336610

Positions:

• chr13-91352883-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000582141.6(MIR17HG):​n.3326C>T 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 0.472 in 151,662 control chromosomes in the GnomAD database, including 18,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.47 (18387 hom., cov: 29)
• Consequence: MIR17HG ENST00000582141.6 non_coding_transcript_exon
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.480

Genes affected

MIR17HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 13-91352883-C-T is Benign according to our data. Variant chr13-91352883-C-T is described in ClinVar as [Benign]. Clinvar id is 3060743.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR17HG	NR_027350.1	n.3326C>T		non_coding_transcript_exon_variant	2/2
MIR17HG	NR_027349.1	n.285-1050C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000582141.6	n.3326C>T		non_coding_transcript_exon_variant	2/2	1
MIR17HG	ENST00000400282.7	n.285-1050C>T		intron_variant		1
MIR17HG	ENST00000710412.1	n.1025C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71506 AN: 151546 Hom.: 18375 Cov.: 29

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.472 AC: 71523 AN: 151662 Hom.: 18387 Cov.: 29 AF XY: 0.472 AC XY: 34937 AN XY: 74086

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.515

Alfa AF: 0.496 Hom.: 2451

Bravo AF: 0.473

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

MIR17HG-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 28, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7336610; hg19: chr13-92005137;