dbSNP rs2249632: MIR205HG:n.594A>G (chr1-209431757-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000433108.1(MIR205HG):n.2938A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 209,298 control chromosomes in the GnomAD database, including 35,374 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 0.53 ( 24728 hom., cov: 32)

Exomes 𝑓: 0.59 ( 10646 hom. )

Consequence

MIR205HG
ENST00000433108.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

7 publications found

Variant links:

Genes affected

MIR205HG (HGNC:43562): (MIR205 host gene)

MIR205HG links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000433108.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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 (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433108.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MIR205HG	NR_145434.1	n.564A>G	non_coding_transcript_exon	Exon 4 of 5
MIR205HG	NR_145435.1	n.512A>G	non_coding_transcript_exon	Exon 3 of 4
MIR205HG	NR_145433.1	n.498-447A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR205HG	ENST00000429156.7	TSL:3	n.594A>G	non_coding_transcript_exon	Exon 4 of 5
MIR205HG	ENST00000431096.7	TSL:3	n.515A>G	non_coding_transcript_exon	Exon 3 of 4
MIR205HG	ENST00000433108.1	TSL:2	n.2938A>G	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.532

AC:

80865

AN:

151996

Hom.:

24716

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.810

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.747

Gnomad SAS

AF:

0.652

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.556

GnomAD4 exome

AF:

0.594

AC:

33962

AN:

57182

Hom.:

10646

Cov.:

AF XY:

0.598

AC XY:

17633

AN XY:

29476

show subpopulations

African (AFR)

AF:

0.144

AC:

430

AN:

2994

American (AMR)

AF:

0.656

AC:

2509

AN:

3822

Ashkenazi Jewish (ASJ)

AF:

0.657

AC:

876

AN:

1334

East Asian (EAS)

AF:

0.715

AC:

2706

AN:

3782

South Asian (SAS)

AF:

0.600

AC:

3821

AN:

6370

European-Finnish (FIN)

AF:

0.558

AC:

899

AN:

1612

Middle Eastern (MID)

AF:

0.599

AC:

121

AN:

202

European-Non Finnish (NFE)

AF:

0.612

AC:

20914

AN:

34186

Other (OTH)

AF:

0.585

AC:

1686

AN:

2880

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

562

1124

1687

2249

2811

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

242

484

726

968

1210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.532

AC:

80898

AN:

152116

Hom.:

24728

Cov.:

AF XY:

0.539

AC XY:

40053

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.201

AC:

8332

AN:

41518

American (AMR)

AF:

0.651

AC:

9961

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2380

AN:

3470

East Asian (EAS)

AF:

0.746

AC:

3853

AN:

5162

South Asian (SAS)

AF:

0.653

AC:

3147

AN:

4816

European-Finnish (FIN)

AF:

0.645

AC:

6833

AN:

10590

Middle Eastern (MID)

AF:

0.633

AC:

186

AN:

294

European-Non Finnish (NFE)

AF:

0.652

AC:

44287

AN:

67956

Other (OTH)

AF:

0.561

AC:

1182

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1684

3368

5051

6735

8419

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

698

1396

2094

2792

3490

<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:

0.553

Hom.:

5519

Bravo

AF:

0.521

Asia WGS

AF:

0.654

AC:

2277

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.61

PhyloP100

-0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over