rs6542147

Positions:

• chr2-113583086-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_031632.1(MIR1302-3):​n.11C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.49 (0 hom., cov: 64)
  • Exomes 𝑓: 0.49 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1302-3 NR_031632.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

MIR1302-3 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1302-3	NR_031632.1	n.11C>T		non_coding_transcript_exon_variant	1/1
LOC124907875	XR_007087203.1	n.961C>T		non_coding_transcript_exon_variant	1/2
LOC124907875	XR_007087204.1	n.945C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1302-3	ENST00000408128.1	n.11C>T		non_coding_transcript_exon_variant	1/1	6
ENSG00000287165	ENST00000666960.1	n.67C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 72937 AN: 148014 Hom.: 0 Cov.: 64 FAILED QC

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.492

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.489 AC: 172254 AN: 352164 Hom.: 0 Cov.: 0 AF XY: 0.489 AC XY: 97685 AN XY: 199958

Gnomad4 AFR exome AF: 0.498

Gnomad4 AMR exome AF: 0.493

Gnomad4 ASJ exome AF: 0.487

Gnomad4 EAS exome AF: 0.498

Gnomad4 SAS exome AF: 0.487

Gnomad4 FIN exome AF: 0.494

Gnomad4 NFE exome AF: 0.487

Gnomad4 OTH exome AF: 0.489

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.493 AC: 72997 AN: 148136 Hom.: 0 Cov.: 64 AF XY: 0.493 AC XY: 35684 AN XY: 72384

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.492

Alfa AF: 0.482 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6542147; hg19: chr2-114340663;