dbSNP rs7944477: MIR4300HG:n.941-22885G>T (chr11-81905181-C-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.941-22885G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0708 in 152,032 control chromosomes in the GnomAD database, including 562 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 0.071 ( 562 hom., cov: 32)

Consequence

MIR4300HG
ENST00000500502.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.620

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1 link	n.941-22885G>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR4300HG	ENST00000500502.5 link	n.941-22885G>T	intron_variant	Intron 6 of 7	1
MIR4300HG	ENST00000530896.6 link	n.473-22885G>T	intron_variant	Intron 3 of 4	3
MIR4300HG	ENST00000653173.1 link	n.419-80250G>T	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0706

AC:

10728

AN:

151914

Hom.:

557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.0544

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.0209

Gnomad FIN

AF:

0.0207

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0468

Gnomad OTH

AF:

0.0627

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

GnomAD4 genome

AF:

0.0708

AC:

10759

AN:

152032

Hom.:

562

Cov.:

AF XY:

0.0679

AC XY:

5050

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.143

AC:

5931

AN:

41470

American (AMR)

AF:

0.0543

AC:

827

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.0542

AC:

188

AN:

3470

East Asian (EAS)

AF:

0.000581

AC:

AN:

5164

South Asian (SAS)

AF:

0.0205

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0207

AC:

219

AN:

10600

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0468

AC:

3180

AN:

67946

Other (OTH)

AF:

0.0625

AC:

132

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

507

1014

1520

2027

2534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0606

Hom.:

Bravo

AF:

0.0769

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.27

(source)

DANN

Benign

0.69

PhyloP100

-0.62

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