rs3008994

Positions:

• chr3-75630794-C-A
• chr3-75630794-C-G
• chr3-75630794-C-T

Variant summary

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

The NR_031714.1(MIR1324):​n.32C>A 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 0.00102 in 152,038 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 0.0010 (0 hom., cov: 62)
  • Exomes 𝑓: 0.0013 (0 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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00103 AC: 156 AN: 151920 Hom.: 0 Cov.: 62

Gnomad AFR AF: 0.000822

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000525

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00686

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00103

Gnomad OTH AF: 0.00240

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00134 AC: 498 AN: 372156 Hom.: 0 Cov.: 0 AF XY: 0.00160 AC XY: 339 AN XY: 211510

Gnomad4 AFR exome AF: 0.000294

Gnomad4 AMR exome AF: 0.000172

Gnomad4 ASJ exome AF: 0.000613

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00496

Gnomad4 FIN exome AF: 0.000159

Gnomad4 NFE exome AF: 0.000684

Gnomad4 OTH exome AF: 0.00111

GnomAD4 genome AF: 0.00102 AC: 155 AN: 152038 Hom.: 0 Cov.: 62 AF XY: 0.00106 AC XY: 79 AN XY: 74318

Gnomad4 AFR AF: 0.000820

Gnomad4 AMR AF: 0.000524

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00665

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00103

Gnomad4 OTH AF: 0.00238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.8
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;