13-91351334-C-T

Position:

• chr13-91351334-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000581816.1(MIR17HG):​n.1270C>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 0.000135 in 531,502 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00033 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000058 (0 hom.)
• Consequence: MIR17HG ENST00000581816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

MIR17HG (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR17HG	NR_027350.1	n.1777C>T		non_coding_transcript_exon_variant	2/2
MIR92A1	NR_029508.1	n.21C>T		non_coding_transcript_exon_variant	1/1
MIR92A1	unassigned_transcript_2148	n.11C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000581816.1	n.1270C>T		non_coding_transcript_exon_variant	3/3	1
MIR17HG	ENST00000582141.6	n.1777C>T		non_coding_transcript_exon_variant	2/2	1
MIR17HG	ENST00000400282.7	n.284+1108C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.000329 AC: 50 AN: 152160 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.0000757 AC: 19 AN: 251074 Hom.: 0 AF XY: 0.0000441 AC XY: 6 AN XY: 135912

Gnomad AFR exome AF: 0.000988

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000882

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000580 AC: 22 AN: 379342 Hom.: 0 Cov.: 0 AF XY: 0.0000418 AC XY: 9 AN XY: 215384

Gnomad4 AFR exome AF: 0.00115

Gnomad4 AMR exome AF: 0.0000828

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000300

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000528

Gnomad4 OTH exome AF: 0.000241

GnomAD4 genome AF: 0.000329 AC: 50 AN: 152160 Hom.: 0 Cov.: 33 AF XY: 0.000296 AC XY: 22 AN XY: 74332

Gnomad4 AFR AF: 0.00101

Gnomad4 AMR AF: 0.000393

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000132 Hom.: 0

Bravo AF: 0.000412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	19
DANN	Benign	0.86
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: rs72631821; hg19: chr13-92003588;