Genetic Variant MIR4435-2HG:n.340-8244A>G (chr2-111173844-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 ENST00000642191.1(MIR4435-2HG):n.340-8244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,190 control chromosomes in the GnomAD database, including 1,945 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 0.15 ( 1945 hom., cov: 33)

Consequence

MIR4435-2HG
ENST00000642191.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

11 publications found

Variant links:

Genes affected

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

MIR4435-2HG 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MIR4435-2HG	ENST00000642191.1 link	n.340-8244A>G	intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645030.2 link	n.453-136922A>G	intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645051.2 link	n.450-8214A>G	intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000673798.1 link	n.652-41589A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22940

AN:

152072

Hom.:

1940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0644

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.0871

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.151

AC:

22963

AN:

152190

Hom.:

1945

Cov.:

AF XY:

0.146

AC XY:

10842

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.116

AC:

4830

AN:

41530

American (AMR)

AF:

0.104

AC:

1595

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0644

AC:

223

AN:

3464

East Asian (EAS)

AF:

0.247

AC:

1280

AN:

5174

South Asian (SAS)

AF:

0.0870

AC:

419

AN:

4818

European-Finnish (FIN)

AF:

0.154

AC:

1635

AN:

10608

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12495

AN:

67984

Other (OTH)

AF:

0.124

AC:

262

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1013

2025

3038

4050

5063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.171

Hom.:

2810

Bravo

AF:

0.149

Asia WGS

AF:

0.176

AC:

612

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.4

(source)

DANN

Benign

0.54

PhyloP100

0.049

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