rs11316732

chr21-41167642-AC-Achr21-41167642-ACC-A

Variant summary

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

The 21-41167642-AC-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,080 control chromosomes in the GnomAD database, including 6,887 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.30 (6829 hom., cov: 0)
  • Exomes 𝑓: 0.38 (58 hom.)
• Consequence: MIR3197 NR_036167.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

Genes affected

MIR3197 (HGNC:38366): (microRNA 3197) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3197	NR_036167.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3197	ENST00000582241.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.297 AC: 44925 AN: 151044 Hom.: 6809 Cov.: 0

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.292

GnomAD3 exomes AF: 0.324 AC: 447 AN: 1380 Hom.: 51 AF XY: 0.313 AC XY: 232 AN XY: 742

Gnomad AFR exome AF: 0.364

Gnomad AMR exome AF: 0.389

Gnomad ASJ exome AF: 0.417

Gnomad EAS exome AF: 0.250

Gnomad SAS exome AF: 0.429

Gnomad NFE exome AF: 0.321

Gnomad OTH exome AF: 0.294

GnomAD4 exome AF: 0.384 AC: 356 AN: 926 Hom.: 58 Cov.: 0 AF XY: 0.381 AC XY: 170 AN XY: 446

Gnomad4 AFR exome AF: 0.450

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.571

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.268

Gnomad4 OTH exome AF: 0.329

GnomAD4 genome AF: 0.298 AC: 44976 AN: 151154 Hom.: 6829 Cov.: 0 AF XY: 0.300 AC XY: 22159 AN XY: 73832

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.300

Alfa AF: 0.280 Hom.: 733

Bravo AF: 0.298

Asia WGS AF: 0.399 AC: 1385 AN: 3476

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: rs11316732; hg19: chr21-42539569;