rs12803915

Positions:

• chr11-65444508-G-A

Variant summary

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

The NR_030343.1(MIR612):​n.51G>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 0.17 in 490,522 control chromosomes in the GnomAD database, including 7,664 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 0.17 (2285 hom., cov: 30)
  • Exomes 𝑓: 0.17 (5379 hom.)
• Consequence: MIR612 NR_030343.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

MIR612 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR612	NR_030343.1	n.51G>A		non_coding_transcript_exon_variant	1/1
NEAT1	NR_131012.1	n.21711G>A		non_coding_transcript_exon_variant	1/1
MIR612	unassigned_transcript_1908	n.*11G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR612	ENST00000384994.1	n.51G>A		non_coding_transcript_exon_variant	1/1	6
NEAT1	ENST00000501122.2	n.21711G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25323 AN: 151834 Hom.: 2283 Cov.: 30

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.159

GnomAD3 exomes AF: 0.164 AC: 29712 AN: 180892 Hom.: 2663 AF XY: 0.164 AC XY: 15893 AN XY: 96738

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.130

Gnomad ASJ exome AF: 0.193

Gnomad EAS exome AF: 0.146

Gnomad SAS exome AF: 0.118

Gnomad FIN exome AF: 0.121

Gnomad NFE exome AF: 0.207

Gnomad OTH exome AF: 0.178

GnomAD4 exome AF: 0.172 AC: 58085 AN: 338566 Hom.: 5379 Cov.: 0 AF XY: 0.169 AC XY: 32339 AN XY: 191724

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.131

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.142

Gnomad4 SAS exome AF: 0.118

Gnomad4 FIN exome AF: 0.124

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.181

GnomAD4 genome AF: 0.167 AC: 25341 AN: 151956 Hom.: 2285 Cov.: 30 AF XY: 0.159 AC XY: 11838 AN XY: 74264

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.156

Alfa AF: 0.193 Hom.: 1493

Bravo AF: 0.170

Asia WGS AF: 0.113 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.7
DANN	Benign	0.79
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12803915; hg19: chr11-65211979; COSMIC: COSV66057836;