rs11231898

chr11-64891364-G-A

Variant summary

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

The NR_029829.1(MIR194-2):n.76C>T 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 0.00725 in 521,136 control chromosomes in the GnomAD database, including 139 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 0.019 (106 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (33 hom.)
• Consequence: MIR194-2 NR_029829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758

Genes affected

MIR194-2 (HGNC:31565): (microRNA 194-2) 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]

MIR194-2HG (HGNC:51946): (MIR194-2 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR194-2	NR_029829.1	n.76C>T		non_coding_transcript_exon_variant	1/1
MIR194-2HG	NR_133640.1	n.276+1226C>T		intron_variant, non_coding_transcript_variant
MIR194-2HG	NR_133638.1	n.1843C>T		non_coding_transcript_exon_variant	2/2
MIR194-2HG	NR_133639.1	n.437+1065C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR194-2	ENST00000384864.1	n.76C>T		non_coding_transcript_exon_variant	1/1
MIR194-2HG	ENST00000710930.1	n.551+1065C>T		intron_variant, non_coding_transcript_variant
MIR194-2HG	ENST00000413053.2	n.1843C>T		non_coding_transcript_exon_variant	2/2	2
MIR194-2HG	ENST00000710929.1	n.390+1226C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2838 AN: 152014 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0148

GnomAD3 exomes AF: 0.00484 AC: 1090 AN: 225156 Hom.: 32 AF XY: 0.00353 AC XY: 432 AN XY: 122504

Gnomad AFR exome AF: 0.0654

Gnomad AMR exome AF: 0.00360

Gnomad ASJ exome AF: 0.00265

Gnomad EAS exome AF: 0.000469

Gnomad SAS exome AF: 0.0000713

Gnomad FIN exome AF: 0.0000524

Gnomad NFE exome AF: 0.000261

Gnomad OTH exome AF: 0.00252

GnomAD4 exome AF: 0.00254 AC: 936 AN: 369004 Hom.: 33 Cov.: 0 AF XY: 0.00187 AC XY: 393 AN XY: 209762

Gnomad4 AFR exome AF: 0.0662

Gnomad4 AMR exome AF: 0.00363

Gnomad4 ASJ exome AF: 0.00237

Gnomad4 EAS exome AF: 0.000238

Gnomad4 SAS exome AF: 0.0000619

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000178

Gnomad4 OTH exome AF: 0.00336

GnomAD4 genome AF: 0.0187 AC: 2844 AN: 152132 Hom.: 106 Cov.: 32 AF XY: 0.0176 AC XY: 1311 AN XY: 74364

Gnomad4 AFR AF: 0.0642

Gnomad4 AMR AF: 0.00778

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000294

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.00560 Hom.: 29

Bravo AF: 0.0209

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11231898; hg19: chr11-64658836;