6-33207798-C-T

Variant names:

• chr6-33207798-C-T
• rs107822
• ENST00000692840.2:n.841G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692840.2(ENSG00000288751):​n.841G>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: ENSG00000288751 ENST00000692840.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 56 publications found

Genes affected

ENSG00000288751 (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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692840.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR219A1	NR_029633.1		n.-37C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288751	ENST00000692840.2		n.841G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000306895	ENST00000821858.1		n.850C>T		non_coding_transcript_exon	Exon 1 of 1
	MIR219A1	ENST00000362166.1	TSL:6	n.-37C>T		upstream_gene	N/A

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

GnomAD2 exomes AF: 0.274 AC: 41168 AN: 150316 AF XY: 0.273

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 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

African (AFR) AF: 0.353 AC: 2972 AN: 8428

American (AMR) AF: 0.190 AC: 4778 AN: 25170

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 1686 AN: 9302

East Asian (EAS) AF: 0.628 AC: 5908 AN: 9414

South Asian (SAS) AF: 0.294 AC: 16556 AN: 56222

European-Finnish (FIN) AF: 0.257 AC: 7041 AN: 27398

Middle Eastern (MID) AF: 0.279 AC: 736 AN: 2636

European-Non Finnish (NFE) AF: 0.225 AC: 31850 AN: 141276

Other (OTH) AF: 0.257 AC: 3254 AN: 12652

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

African (AFR) AF: 0.365 AC: 15098 AN: 41404

American (AMR) AF: 0.230 AC: 3517 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3466

East Asian (EAS) AF: 0.637 AC: 3274 AN: 5136

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2865 AN: 10570

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16021 AN: 67910

Other (OTH) AF: 0.306 AC: 646 AN: 2108

Alfa AF: 0.251 Hom.: 6455

Bravo AF: 0.293

Asia WGS AF: 0.389 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs107822; hg19: chr6-33175575;