rs9348512

chr6-10456473-C-A

Variant summary

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

The NR_132993.1(MIR5689HG):n.348C>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 0.339 in 152,156 control chromosomes in the GnomAD database, including 9,056 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 0.34 (9055 hom., cov: 32)
  • Exomes 𝑓: 0.27 (1 hom.)
• Consequence: MIR5689HG NR_132993.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

MIR5689HG (HGNC:52007): (MIR5689 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR5689HG	NR_132993.1	n.348C>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR5689HG	ENST00000366312.2	n.348C>A		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51544 AN: 152016 Hom.: 9058 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.273 AC: 6 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.339 AC: 51582 AN: 152134 Hom.: 9055 Cov.: 32 AF XY: 0.340 AC XY: 25294 AN XY: 74376

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.325

Alfa AF: 0.343 Hom.: 12419

Bravo AF: 0.340

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9348512; hg19: chr6-10456706;