ENST00000692840.2:n.592T>C

Variant names:

• chr6-33208047-A-G
• rs213210
• ENST00000692840.2:n.592T>C

Variant summary

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

The ENST00000692840.2(ENSG00000288751):​n.592T>C 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 0.0945 in 334,434 control chromosomes in the GnomAD database, including 2,845 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 0.093 (1201 hom., cov: 32)
  • Exomes 𝑓: 0.095 (1644 hom.)
• Consequence: ENSG00000288751 ENST00000692840.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 66 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR219A1	NR_029633.1	n.*103A>G		downstream_gene_variant
MIR219A1	unassigned_transcript_1108	n.*172A>G		downstream_gene_variant
MIR219A1	unassigned_transcript_1109	n.*130A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288751	ENST00000692840.2	n.592T>C		non_coding_transcript_exon_variant	Exon 1 of 1
MIR219A1	ENST00000362166.1	n.*103A>G		downstream_gene_variant		6
ENSG00000306895	ENST00000821858.1	n.*193A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14180 AN: 152068 Hom.: 1190 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0955 AC: 17401 AN: 182248 Hom.: 1644 AF XY: 0.0931 AC XY: 9658 AN XY: 103714

African (AFR) AF: 0.0833 AC: 406 AN: 4874

American (AMR) AF: 0.0894 AC: 853 AN: 9544

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 225 AN: 5038

East Asian (EAS) AF: 0.523 AC: 4204 AN: 8038

South Asian (SAS) AF: 0.0822 AC: 2842 AN: 34588

European-Finnish (FIN) AF: 0.0798 AC: 1708 AN: 21412

Middle Eastern (MID) AF: 0.0714 AC: 104 AN: 1456

European-Non Finnish (NFE) AF: 0.0709 AC: 6313 AN: 89082

Other (OTH) AF: 0.0908 AC: 746 AN: 8216

GnomAD4 genome AF: 0.0933 AC: 14198 AN: 152186 Hom.: 1201 Cov.: 32 AF XY: 0.0949 AC XY: 7064 AN XY: 74402

African (AFR) AF: 0.0907 AC: 3766 AN: 41538

American (AMR) AF: 0.0836 AC: 1279 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.513 AC: 2630 AN: 5124

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4822

European-Finnish (FIN) AF: 0.0852 AC: 904 AN: 10616

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0693 AC: 4711 AN: 67994

Other (OTH) AF: 0.119 AC: 251 AN: 2112

Alfa AF: 0.0826 Hom.: 2497

Bravo AF: 0.0975

Asia WGS AF: 0.241 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.93
DANN	Benign	0.37
PhyloP100		-1.3
PromoterAI		0.031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs213210; hg19: chr6-33175824;