rs107822

Positions:

• chr6-33207798-C-T

Variant summary

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

The ENST00000692840.1(ENSG00000288751):​n.676G>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 0.267 in 444,390 control chromosomes in the GnomAD database, including 18,097 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 0.29 (7003 hom., cov: 31)
  • Exomes 𝑓: 0.26 (11094 hom.)
• Consequence: ENST00000692840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

(HGNC:):

MIR219A1 (HGNC:31597): (microRNA 219a-1) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR219A1	NR_029633.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000692840.1	n.676G>A		non_coding_transcript_exon_variant	1/1
MIR219A1	ENST00000362166.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43578 AN: 151774 Hom.: 6976 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.298

GnomAD3 exomes AF: 0.274 AC: 41168 AN: 150316 Hom.: 6831 AF XY: 0.273 AC XY: 21745 AN XY: 79634

Gnomad AFR exome AF: 0.359

Gnomad AMR exome AF: 0.188

Gnomad ASJ exome AF: 0.178

Gnomad EAS exome AF: 0.633

Gnomad SAS exome AF: 0.296

Gnomad FIN exome AF: 0.257

Gnomad NFE exome AF: 0.232

Gnomad OTH exome AF: 0.259

GnomAD4 exome AF: 0.256 AC: 74781 AN: 292498 Hom.: 11094 Cov.: 0 AF XY: 0.258 AC XY: 43271 AN XY: 167650

Gnomad4 AFR exome AF: 0.353

Gnomad4 AMR exome AF: 0.190

Gnomad4 ASJ exome AF: 0.181

Gnomad4 EAS exome AF: 0.628

Gnomad4 SAS exome AF: 0.294

Gnomad4 FIN exome AF: 0.257

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.257

GnomAD4 genome AF: 0.287 AC: 43653 AN: 151892 Hom.: 7003 Cov.: 31 AF XY: 0.289 AC XY: 21458 AN XY: 74202

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.306

Alfa AF: 0.240 Hom.: 3051

Bravo AF: 0.293

Asia WGS AF: 0.389 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs107822; hg19: chr6-33175575;