rs2187473

Variant names:

• chr11-111513121-C-G
• rs2187473
• ENST00000651138.2:n.382C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-111513121-C-G
• chr11-111513121-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000651138.2(MIR34BHG):​n.382C>G 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 0.0000296 in 405,880 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000039 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000024 (0 hom.)
• Consequence: MIR34BHG ENST00000651138.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 17 publications found

Genes affected

MIR34BHG (HGNC:55987): (MIR34B and MIR34C host gene)

BTG4 (HGNC:13862): (BTG anti-proliferation factor 4) The protein encoded by this gene is a member of the BTG/Tob family. This family has structurally related proteins that appear to have antiproliferative properties. This encoded protein can induce G1 arrest in the cell cycle. [provided by RefSeq, Jul 2008]

MIR34B (HGNC:31636): (microRNA 34b) 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR34BHG	NR_147706.1	n.375C>G		non_coding_transcript_exon_variant	Exon 2 of 2
BTG4	NM_001367974.1	c.-27+1546G>C		intron_variant	Intron 1 of 4		NP_001354903.1
BTG4	XM_024448589.2	c.-27+1546G>C		intron_variant	Intron 1 of 7		XP_024304357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR34BHG	ENST00000651138.2	n.382C>G		non_coding_transcript_exon_variant	Exon 2 of 2
MIR34BHG	ENST00000726427.1	n.489C>G		non_coding_transcript_exon_variant	Exon 3 of 3
BTG4	ENST00000689553.1	c.-207-844G>C		intron_variant	Intron 1 of 6			ENSP00000508793.1
MIR34B	ENST00000385076.3	n.*100C>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0000394 AC: 6 AN: 152130 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000236 AC: 6 AN: 253750 Hom.: 0 AF XY: 0.0000216 AC XY: 3 AN XY: 138956

African (AFR) AF: 0.00 AC: 0 AN: 6236

American (AMR) AF: 0.00 AC: 0 AN: 20650

Ashkenazi Jewish (ASJ) AF: 0.000612 AC: 5 AN: 8174

East Asian (EAS) AF: 0.00 AC: 0 AN: 7454

South Asian (SAS) AF: 0.00 AC: 0 AN: 51076

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25456

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1036

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 122288

Other (OTH) AF: 0.0000879 AC: 1 AN: 11380

GnomAD4 genome AF: 0.0000394 AC: 6 AN: 152130 Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2 AN XY: 74314

African (AFR) AF: 0.0000241 AC: 1 AN: 41434

American (AMR) AF: 0.00 AC: 0 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68012

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.00 Hom.: 114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.29
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs2187473; hg19: chr11-111383846;