rs41291173

Variant names:

• chr2-55983005-G-A
• rs41291173
• ENST00000606639.1:n.82+30766G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-55983005-G-A
• chr2-55983005-G-C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BS1 BS2

The NR_029630.1(MIR217):​n.72C>T variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 532,846 control chromosomes in the GnomAD database, including 86 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 0.014 (25 hom., cov: 32)
  • Exomes 𝑓: 0.014 (61 hom.)
• Consequence: MIR217 NR_029630.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.46
• Publications: 8 publications found

Genes affected

ENSG00000272180 (HGNC:):

MIR217 (HGNC:31594): (microRNA 217) 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]

MIR217HG (HGNC:50537): (MIR217 host gene)

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0141 (2152/152268) while in subpopulation AMR AF = 0.0275 (421/15310). AF 95% confidence interval is 0.0253. There are 25 homozygotes in GnomAd4. There are 985 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 25 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_029630.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR217	NR_029630.1		n.72C>T		non_coding_transcript_exon	Exon 1 of 1
	MIR217HG	NR_126406.1		n.209-19123C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272180	ENST00000606639.1	TSL:1	n.82+30766G>A		intron	N/A
	MIR217	ENST00000384817.3	TSL:6	n.72C>T		non_coding_transcript_exon	Exon 1 of 1
	MIR217HG	ENST00000446139.2	TSL:5	n.925-19123C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0142 AC: 2153 AN: 152150 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00500

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00679

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0230

GnomAD2 exomes AF: 0.0135 AC: 3356 AN: 247852 AF XY: 0.0135

Gnomad AFR exome AF: 0.00420

Gnomad AMR exome AF: 0.0162

Gnomad ASJ exome AF: 0.00511

Gnomad EAS exome AF: 0.000110

Gnomad FIN exome AF: 0.00947

Gnomad NFE exome AF: 0.0202

Gnomad OTH exome AF: 0.0156

GnomAD4 exome AF: 0.0140 AC: 5338 AN: 380578 Hom.: 61 Cov.: 0 AF XY: 0.0133 AC XY: 2888 AN XY: 216602

African (AFR) AF: 0.00392 AC: 41 AN: 10460

American (AMR) AF: 0.0161 AC: 577 AN: 35938

Ashkenazi Jewish (ASJ) AF: 0.00496 AC: 58 AN: 11700

East Asian (EAS) AF: 0.00 AC: 0 AN: 13088

South Asian (SAS) AF: 0.00420 AC: 278 AN: 66134

European-Finnish (FIN) AF: 0.0101 AC: 327 AN: 32222

Middle Eastern (MID) AF: 0.00847 AC: 24 AN: 2834

European-Non Finnish (NFE) AF: 0.0198 AC: 3799 AN: 191540

Other (OTH) AF: 0.0140 AC: 234 AN: 16662

GnomAD4 genome AF: 0.0141 AC: 2152 AN: 152268 Hom.: 25 Cov.: 32 AF XY: 0.0132 AC XY: 985 AN XY: 74458

African (AFR) AF: 0.00498 AC: 207 AN: 41556

American (AMR) AF: 0.0275 AC: 421 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00291 AC: 14 AN: 4818

European-Finnish (FIN) AF: 0.00679 AC: 72 AN: 10610

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0201 AC: 1366 AN: 68004

Other (OTH) AF: 0.0227 AC: 48 AN: 2112

Alfa AF: 0.0137 Hom.: 4

Bravo AF: 0.0146

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Benign	0.87
PhyloP100		7.5

Splicing

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

Other links and lift over

dbSNP: rs41291173; hg19: chr2-56210140;