dbSNP rs2175961: MIR4300HG:n.431+19121A>G (chr11-82330805-T-C) – 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+19121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,098 control chromosomes in the GnomAD database, including 1,307 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 0.12 ( 1307 hom., cov: 33)

Consequence

MIR4300HG
ENST00000500502.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1 link	n.431+19121A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR4300HG	ENST00000500502.5 link	n.431+19121A>G	intron_variant	Intron 3 of 7	1
MIR4300HG	ENST00000532217.1 link	n.557+25707A>G	intron_variant	Intron 4 of 4	5
MIR4300HG	ENST00000653173.1 link	n.184+25707A>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18513

AN:

151980

Hom.:

1304

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.0992

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0412

Gnomad FIN

AF:

0.0573

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.130

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

GnomAD4 genome

AF:

0.122

AC:

18531

AN:

152098

Hom.:

1307

Cov.:

AF XY:

0.119

AC XY:

8852

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.191

AC:

7920

AN:

41494

American (AMR)

AF:

0.109

AC:

1672

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0992

AC:

344

AN:

3468

East Asian (EAS)

AF:

0.00174

AC:

AN:

5180

South Asian (SAS)

AF:

0.0408

AC:

197

AN:

4826

European-Finnish (FIN)

AF:

0.0573

AC:

608

AN:

10602

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7256

AN:

67934

Other (OTH)

AF:

0.129

AC:

273

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

854

1709

2563

3418

4272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.121

Hom.:

158

Bravo

AF:

0.129

Asia WGS

AF:

0.0330

AC:

117

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

(source)

DANN

Benign

0.73

PhyloP100

0.21

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