dbSNP rs135771: MIR3667HG:n.101-102324C>T (chr22-49543536-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000414287.5(MIR3667HG):n.101-102324C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 154,486 control chromosomes in the GnomAD database, including 2,484 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 0.16 ( 2464 hom., cov: 32)

Exomes 𝑓: 0.10 ( 20 hom. )

Consequence

MIR3667HG
ENST00000414287.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281

Variant links:

Genes affected

MIR3667HG (HGNC:28010): (MIR3667 host gene)

MIR3667HG links:

MIR3667 (HGNC:38990): (microRNA 3667) 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]

MIR3667 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR3667HG	NR_110522.2 link	n.115+113869C>T	intron_variant	Intron 1 of 2
MIR3667HG	NR_110523.2 link	n.116-102324C>T	intron_variant	Intron 1 of 4
MIR3667	NR_037440.1 link	n.-70C>T	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR3667HG	ENST00000414287.5 link	n.101-102324C>T	intron_variant	Intron 1 of 4	1
MIR3667HG	ENST00000416411.1 link	n.54-102324C>T	intron_variant	Intron 1 of 2	4
MIR3667	ENST00000581025.1 link	n.-70C>T	upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24514

AN:

151866

Hom.:

2463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0569

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.154

GnomAD4 exome

AF:

0.102

AC:

255

AN:

2502

Hom.:

AF XY:

0.0997

AC XY:

128

AN XY:

1284

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.0545

Gnomad4 NFE exome

AF:

0.0924

Gnomad4 OTH exome

AF:

0.177

GnomAD4 genome

AF:

0.162

AC:

24546

AN:

151984

Hom.:

2464

Cov.:

AF XY:

0.159

AC XY:

11835

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.272

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.306

Gnomad4 SAS

AF:

0.114

Gnomad4 FIN

AF:

0.0569

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.152

Hom.:

324

Bravo

AF:

0.174

Asia WGS

AF:

0.208

AC:

725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.37

DANN

Benign

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over