Genetic Variant ENST00000427348.5:n.111+935A>G (chr20-26208188-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000427348.5(MIR663AHG):n.111+935A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MIR663AHG
ENST00000427348.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

5 publications found

Variant links:

COSMIC-nc: COSV66109777

Genes affected

MIR663AHG (HGNC:27662): (MIR663A host gene)

MIR663AHG links:

MIR663A (HGNC:32919): (microRNA 663a) 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]

MIR663A links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR663A	NR_030386.1 link	n.91A>G	splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1
MIR663AHG	NR_040095.1 link	n.111+935A>G	intron_variant	Intron 1 of 4
MIR663A	unassigned_transcript_3435	n.*55A>G	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR663AHG	ENST00000427348.5 link	n.111+935A>G	intron_variant	Intron 1 of 4	1
MIR663A	ENST00000385250.1 link	n.91A>G	splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR663AHG	ENST00000596111.6 link	n.63A>G	non_coding_transcript_exon_variant	Exon 1 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

137060

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

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

GnomAD2 exomes

AF:

0.00

AC:

AN:

92482

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

230024

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

135944

African (AFR)

AF:

0.00

AC:

AN:

4082

American (AMR)

AF:

0.00

AC:

AN:

19546

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8598

East Asian (EAS)

AF:

0.00

AC:

AN:

2320

South Asian (SAS)

AF:

0.00

AC:

AN:

50200

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10750

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1218

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

122862

Other (OTH)

AF:

0.00

AC:

AN:

10448

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

137060

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

66814

African (AFR)

AF:

0.00

AC:

AN:

37378

American (AMR)

AF:

0.00

AC:

AN:

13928

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3226

East Asian (EAS)

AF:

0.00

AC:

AN:

4550

South Asian (SAS)

AF:

0.00

AC:

AN:

4172

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9328

Middle Eastern (MID)

AF:

0.00

AC:

AN:

304

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

61528

Other (OTH)

AF:

0.00

AC:

AN:

1854

Alfa

AF:

0.000340

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

7.6

(source)

DANN

Benign

0.18

PhyloP100

-1.2

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over