Genetic Variant MIR4300HG:n.431+50096C>T (chr11-82299830-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000500502.5(MIR4300HG):n.431+50096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,984 control chromosomes in the GnomAD database, including 920 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 0.11 ( 920 hom., cov: 32)

Consequence

MIR4300HG
ENST00000500502.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500

Publications

1 publications found

Variant links:

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

MIR4300HG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1 link	n.431+50096C>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR4300HG	ENST00000500502.5 link	n.431+50096C>T	intron_variant	Intron 3 of 7	1
MIR4300HG	ENST00000532217.1 link	n.557+56682C>T	intron_variant	Intron 4 of 4	5
MIR4300HG	ENST00000653173.1 link	n.184+56682C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

16012

AN:

151866

Hom.:

919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.0940

Gnomad ASJ

AF:

0.0939

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0373

Gnomad FIN

AF:

0.0571

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.114

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.105

AC:

16021

AN:

151984

Hom.:

920

Cov.:

AF XY:

0.103

AC XY:

7619

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.139

AC:

5769

AN:

41468

American (AMR)

AF:

0.0938

AC:

1430

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.0939

AC:

326

AN:

3470

East Asian (EAS)

AF:

0.00155

AC:

AN:

5176

South Asian (SAS)

AF:

0.0369

AC:

178

AN:

4824

European-Finnish (FIN)

AF:

0.0571

AC:

605

AN:

10598

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7225

AN:

67888

Other (OTH)

AF:

0.113

AC:

237

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

740

1479

2219

2958

3698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0622

Hom.:

Bravo

AF:

0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.9

(source)

DANN

Benign

0.72

PhyloP100

-0.0050

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over