14-101066756-C-T

Position:

• chr14-101066756-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_030392.1(MIR656):​n.33C>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 0.0496 in 534,688 control chromosomes in the GnomAD database, including 1,214 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 0.069 (667 hom., cov: 33)
  • Exomes 𝑓: 0.042 (547 hom.)
• Consequence: MIR656 NR_030392.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

Genes affected

MIR656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR656	NR_030392.1	n.33C>T		non_coding_transcript_exon_variant	1/1
MIR656	unassigned_transcript_2453	n.-10C>T		upstream_gene_variant
MIR656	unassigned_transcript_2452	n.*5C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR656	ENST00000385224.1	n.33C>T		non_coding_transcript_exon_variant	1/1	6
MEG9	ENST00000699461.1	n.497-3686C>T		intron_variant
MEG9	ENST00000699462.1	n.219+2389C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0688 AC: 10471 AN: 152146 Hom.: 666 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0502

GnomAD3 exomes AF: 0.0462 AC: 11598 AN: 251018 Hom.: 494 AF XY: 0.0443 AC XY: 6021 AN XY: 135876

Gnomad AFR exome AF: 0.170

Gnomad AMR exome AF: 0.0459

Gnomad ASJ exome AF: 0.00756

Gnomad EAS exome AF: 0.0417

Gnomad SAS exome AF: 0.0688

Gnomad FIN exome AF: 0.0339

Gnomad NFE exome AF: 0.0295

Gnomad OTH exome AF: 0.0390

GnomAD4 exome AF: 0.0419 AC: 16012 AN: 382424 Hom.: 547 Cov.: 0 AF XY: 0.0421 AC XY: 9176 AN XY: 217714

Gnomad4 AFR exome AF: 0.170

Gnomad4 AMR exome AF: 0.0454

Gnomad4 ASJ exome AF: 0.00818

Gnomad4 EAS exome AF: 0.0366

Gnomad4 SAS exome AF: 0.0641

Gnomad4 FIN exome AF: 0.0345

Gnomad4 NFE exome AF: 0.0300

Gnomad4 OTH exome AF: 0.0450

GnomAD4 genome AF: 0.0690 AC: 10502 AN: 152264 Hom.: 667 Cov.: 33 AF XY: 0.0687 AC XY: 5118 AN XY: 74468

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.0658

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0275

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0402 Hom.: 147

Bravo AF: 0.0735

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	17
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58834075; hg19: chr14-101533093; COSMIC: COSV62998613;