Genetic Variant MIRLET7BHG:n.3517C>T (chr22-46112885-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000360737.4(MIRLET7BHG):n.3517C>T 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 0.00000297 in 336,256 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: not found (cov: 33)

Exomes 𝑓: 0.0000030 ( 0 hom. )

Consequence

MIRLET7BHG
ENST00000360737.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.359

Publications

13 publications found

Variant links:

Genes affected

MIRLET7BHG (HGNC:37189): (MIRLET7B host gene)

MIRLET7BHG links:

LOC124905135 (HGNC:):

LOC124905135 links:

MIRLET7A3 (HGNC:31478): (microRNA let-7a-3) 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]

MIRLET7A3 links:

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ACMG classification

Classification was made for transcript

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=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360737.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MIRLET7BHG	NR_027033.2	n.3674C>T	non_coding_transcript_exon	Exon 6 of 6
MIRLET7BHG	NR_110479.1	n.3523C>T	non_coding_transcript_exon	Exon 5 of 5
MIRLET7A3	NR_029478.1	n.*63C>T	downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIRLET7BHG	ENST00000360737.4	TSL:2	n.3517C>T	non_coding_transcript_exon	Exon 5 of 5
MIRLET7BHG	ENST00000794300.1		n.745C>T	non_coding_transcript_exon	Exon 6 of 6
MIRLET7BHG	ENST00000794301.1		n.626C>T	non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000297

AC:

AN:

336256

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

188350

show subpopulations

African (AFR)

AF:

0.000103

AC:

AN:

9704

American (AMR)

AF:

0.00

AC:

AN:

32858

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9950

East Asian (EAS)

AF:

0.00

AC:

AN:

12204

South Asian (SAS)

AF:

0.00

AC:

AN:

62402

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1894

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

163718

Other (OTH)

AF:

0.00

AC:

AN:

14704

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

775

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.56

(source)

DANN

Benign

0.94

PhyloP100

0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over