1-1167183-G-A

Variant names:

• chr1-1167183-G-A
• rs72563729
• ENST00000384997.3:n.80G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000384997.3(MIR200B):​n.80G>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 0.0141 in 531,854 control chromosomes in the GnomAD database, including 94 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 0.012 (20 hom., cov: 33)
  • Exomes 𝑓: 0.015 (74 hom.)
• Consequence: MIR200B ENST00000384997.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 10 publications found

Genes affected

MIR200B (HGNC:31579): (microRNA 200b) 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]

MIR200BHG (HGNC:58145):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0118 (1801/152240) while in subpopulation NFE AF = 0.0198 (1349/67974). AF 95% confidence interval is 0.019. There are 20 homozygotes in GnomAd4. There are 839 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000384997.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR200B	NR_029639.1		n.80G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR200B	ENST00000384997.3	TSL:6	n.80G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0118 AC: 1802 AN: 152122 Hom.: 20 Cov.: 33

Gnomad AFR AF: 0.00292

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00661

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.00773

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.00861

GnomAD2 exomes AF: 0.0127 AC: 3103 AN: 243388 AF XY: 0.0130

Gnomad AFR exome AF: 0.00240

Gnomad AMR exome AF: 0.00633

Gnomad ASJ exome AF: 0.00970

Gnomad EAS exome AF: 0.0000553

Gnomad FIN exome AF: 0.00986

Gnomad NFE exome AF: 0.0182

Gnomad OTH exome AF: 0.0172

GnomAD4 exome AF: 0.0151 AC: 5715 AN: 379614 Hom.: 74 Cov.: 0 AF XY: 0.0156 AC XY: 3378 AN XY: 216124

African (AFR) AF: 0.00257 AC: 27 AN: 10506

American (AMR) AF: 0.00673 AC: 243 AN: 36122

Ashkenazi Jewish (ASJ) AF: 0.0102 AC: 118 AN: 11620

East Asian (EAS) AF: 0.00 AC: 0 AN: 13114

South Asian (SAS) AF: 0.0167 AC: 1111 AN: 66372

European-Finnish (FIN) AF: 0.0100 AC: 311 AN: 31104

Middle Eastern (MID) AF: 0.0166 AC: 47 AN: 2834

European-Non Finnish (NFE) AF: 0.0190 AC: 3635 AN: 191334

Other (OTH) AF: 0.0134 AC: 223 AN: 16608

GnomAD4 genome AF: 0.0118 AC: 1801 AN: 152240 Hom.: 20 Cov.: 33 AF XY: 0.0113 AC XY: 839 AN XY: 74434

African (AFR) AF: 0.00291 AC: 121 AN: 41548

American (AMR) AF: 0.00654 AC: 100 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00951 AC: 33 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4828

European-Finnish (FIN) AF: 0.00773 AC: 82 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0198 AC: 1349 AN: 67974

Other (OTH) AF: 0.00852 AC: 18 AN: 2112

Alfa AF: 0.0145 Hom.: 8

Bravo AF: 0.0103

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
DANN	Benign	0.75
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs72563729; hg19: chr1-1102563;