rs10670323

Positions:

• chr19-53725488-G-GAAAGA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_030207.1(MIR516B2):​n.50_54dupAGAAA 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 0.151 in 152,026 control chromosomes in the GnomAD database, including 2,317 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (2317 hom., cov: 29)
  • Exomes 𝑓: 0.11 (2616 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR516B2 NR_030207.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

MIR516B2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR516B2	NR_030207.1	n.50_54dupAGAAA		non_coding_transcript_exon_variant	1/1
MIR516B2	unassigned_transcript_3369	n.-9_-8insAAAGA		upstream_gene_variant
MIR516B2	unassigned_transcript_3368	n.*10_*11insAAAGA		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR516B2	ENST00000385190.1	n.50_54dupAGAAA		non_coding_transcript_exon_variant	1/1	6
ENSG00000269842	ENST00000710708.1	n.585+12390_585+12394dupAGAAA		intron_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22932 AN: 151908 Hom.: 2309 Cov.: 29

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.132

GnomAD3 exomes AF: 0.0665 AC: 15644 AN: 235408 Hom.: 1117 AF XY: 0.0640 AC XY: 8139 AN XY: 127198

Gnomad AFR exome AF: 0.202

Gnomad AMR exome AF: 0.0320

Gnomad ASJ exome AF: 0.0346

Gnomad EAS exome AF: 0.0468

Gnomad SAS exome AF: 0.0559

Gnomad FIN exome AF: 0.126

Gnomad NFE exome AF: 0.0576

Gnomad OTH exome AF: 0.0590

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.107 AC: 39550 AN: 369680 Hom.: 2616 Cov.: 0 AF XY: 0.107 AC XY: 22384 AN XY: 209112

Gnomad4 AFR exome AF: 0.296

Gnomad4 AMR exome AF: 0.0511

Gnomad4 ASJ exome AF: 0.0681

Gnomad4 EAS exome AF: 0.0631

Gnomad4 SAS exome AF: 0.112

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.101

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.151 AC: 22982 AN: 152026 Hom.: 2317 Cov.: 29 AF XY: 0.151 AC XY: 11195 AN XY: 74328

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0725

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.0641

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.131

Alfa AF: 0.116 Hom.: 240

Bravo AF: 0.150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10670323; hg19: chr19-54228742;