ENST00000606639.1:n.82+36716A>T

Variant names:

• chr2-55988955-A-T
• rs41291179
• ENST00000606639.1:n.82+36716A>T

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.82+36716A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 511,260 control chromosomes in the GnomAD database, including 1,351 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 0.084 (818 hom., cov: 32)
  • Exomes 𝑓: 0.047 (533 hom.)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 22 publications found

Genes affected

ENSG00000272180 (HGNC:):

MIR216A (HGNC:31593): (microRNA 216a) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606639.1. 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
	MIR216A	NR_029629.1		n.105T>A		non_coding_transcript_exon	Exon 1 of 1
	MIR217HG	NR_126406.1		n.208+24654T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272180	ENST00000606639.1	TSL:1	n.82+36716A>T		intron	N/A
	MIR216A	ENST00000385063.1	TSL:6	n.105T>A		non_coding_transcript_exon	Exon 1 of 1
	MIR217HG	ENST00000446139.2	TSL:5	n.924+24654T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12847 AN: 152126 Hom.: 818 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0789

GnomAD2 exomes AF: 0.0503 AC: 12450 AN: 247660 AF XY: 0.0486

Gnomad AFR exome AF: 0.184

Gnomad AMR exome AF: 0.0433

Gnomad ASJ exome AF: 0.0628

Gnomad EAS exome AF: 0.000601

Gnomad FIN exome AF: 0.0242

Gnomad NFE exome AF: 0.0470

Gnomad OTH exome AF: 0.0512

GnomAD4 exome AF: 0.0465 AC: 16697 AN: 359016 Hom.: 533 Cov.: 0 AF XY: 0.0460 AC XY: 9257 AN XY: 201180

African (AFR) AF: 0.178 AC: 1816 AN: 10230

American (AMR) AF: 0.0438 AC: 1555 AN: 35492

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 695 AN: 11424

East Asian (EAS) AF: 0.000636 AC: 8 AN: 12578

South Asian (SAS) AF: 0.0429 AC: 2760 AN: 64324

European-Finnish (FIN) AF: 0.0249 AC: 794 AN: 31886

Middle Eastern (MID) AF: 0.0350 AC: 97 AN: 2774

European-Non Finnish (NFE) AF: 0.0466 AC: 8142 AN: 174616

Other (OTH) AF: 0.0529 AC: 830 AN: 15692

GnomAD4 genome AF: 0.0845 AC: 12863 AN: 152244 Hom.: 818 Cov.: 32 AF XY: 0.0817 AC XY: 6083 AN XY: 74448

African (AFR) AF: 0.180 AC: 7458 AN: 41508

American (AMR) AF: 0.0757 AC: 1158 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4830

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3337 AN: 68018

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0421 Hom.: 59

Bravo AF: 0.0909

Asia WGS AF: 0.0310 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	16
DANN	Benign	0.87
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs41291179; hg19: chr2-56216090;