rs61768480

Variant names:

• chr1-1167770-G-A
• rs61768480
• XR_007065348.1:n.4518G>A

Variant summary

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

The XR_007065348.1(MIR200BHG):​n.4518G>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 0.237 in 464,264 control chromosomes in the GnomAD database, including 14,569 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 0.23 (4562 hom., cov: 33)
  • Exomes 𝑓: 0.24 (10007 hom.)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 2 publications found

Genes affected

MIR200BHG (HGNC:58145):

MIR200A (HGNC:31578): (microRNA 200a) 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000384875.3. 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
	MIR200A	NR_029834.1		n.-93G>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR200A	ENST00000384875.3	TSL:6	n.-93G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34991 AN: 151970 Hom.: 4561 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.241 AC: 75091 AN: 312176 Hom.: 10007 AF XY: 0.239 AC XY: 42282 AN XY: 176630

African (AFR) AF: 0.176 AC: 1499 AN: 8516

American (AMR) AF: 0.118 AC: 3198 AN: 27082

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 2013 AN: 10636

East Asian (EAS) AF: 0.0286 AC: 262 AN: 9154

South Asian (SAS) AF: 0.203 AC: 12055 AN: 59368

European-Finnish (FIN) AF: 0.329 AC: 8088 AN: 24564

Middle Eastern (MID) AF: 0.226 AC: 292 AN: 1292

European-Non Finnish (NFE) AF: 0.281 AC: 44335 AN: 157568

Other (OTH) AF: 0.239 AC: 3349 AN: 13996

GnomAD4 genome AF: 0.230 AC: 35011 AN: 152088 Hom.: 4562 Cov.: 33 AF XY: 0.230 AC XY: 17119 AN XY: 74352

African (AFR) AF: 0.174 AC: 7228 AN: 41498

American (AMR) AF: 0.165 AC: 2516 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3472

East Asian (EAS) AF: 0.0308 AC: 159 AN: 5158

South Asian (SAS) AF: 0.188 AC: 910 AN: 4830

European-Finnish (FIN) AF: 0.341 AC: 3617 AN: 10592

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19158 AN: 67928

Other (OTH) AF: 0.219 AC: 464 AN: 2114

Alfa AF: 0.262 Hom.: 686

Bravo AF: 0.211

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.51
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs61768480; hg19: chr1-1103150;