chr3-75630794-C-G

Position:

• chr3-75630794-C-G

Variant summary

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

The NR_031714.1(MIR1324):​n.32C>G 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 (50 hom., cov: 62)
  • Exomes 𝑓: 0.25 (32 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1324 NR_031714.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

MIR1324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1324	NR_031714.1	n.32C>G		non_coding_transcript_exon_variant	1/1
CLUHP10		n.75630794C>G		intragenic_variant
MIR1324	unassigned_transcript_644	n.-29C>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1324	ENST00000640185.1	n.32C>G		non_coding_transcript_exon_variant	1/1	6
CLUHP10	ENST00000631979.1	n.340+23C>G		intron_variant		6
RPL23AP49	ENST00000638439.1	n.138-593G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 43547 AN: 143996 Hom.: 50 Cov.: 62 FAILED QC

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.254 AC: 78634 AN: 309494 Hom.: 32 Cov.: 0 AF XY: 0.259 AC XY: 45145 AN XY: 174510

Gnomad4 AFR exome AF: 0.296

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.395

Gnomad4 SAS exome AF: 0.341

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.252

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.302 AC: 43562 AN: 144102 Hom.: 50 Cov.: 62 AF XY: 0.303 AC XY: 21276 AN XY: 70246

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.294

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3008994; hg19: chr3-75679945;