rs3008993

Positions:

• chr3-75630855-T-C

Variant summary

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

The NR_031714.1(MIR1324):​n.93T>C 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 0.30 (34 hom., cov: 65)
  • Exomes 𝑓: 0.26 (35 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1324 NR_031714.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

MIR1324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1324	NR_031714.1	n.93T>C		non_coding_transcript_exon_variant	1/1
CLUHP10		n.75630855T>C		intragenic_variant
MIR1324	unassigned_transcript_644	n.*9T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1324	ENST00000640185.1	n.93T>C		non_coding_transcript_exon_variant	1/1	6
CLUHP10	ENST00000631979.1	n.340+84T>C		intron_variant		6
RPL23AP49	ENST00000638439.1	n.138-654A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 41942 AN: 139478 Hom.: 34 Cov.: 65 FAILED QC

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.259 AC: 80041 AN: 309326 Hom.: 35 Cov.: 0 AF XY: 0.264 AC XY: 45967 AN XY: 174176

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.247

Gnomad4 ASJ exome AF: 0.236

Gnomad4 EAS exome AF: 0.398

Gnomad4 SAS exome AF: 0.352

Gnomad4 FIN exome AF: 0.159

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.301 AC: 41960 AN: 139574 Hom.: 34 Cov.: 65 AF XY: 0.301 AC XY: 20475 AN XY: 67976

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.294

Alfa AF: 0.305 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3008993; hg19: chr3-75680006;