Genetic Variant MICD:n.29972595G>A (chr6-29972595-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 variant allele was found at a frequency of 0.133 in 433,556 control chromosomes in the GnomAD database, including 4,540 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 ( 2086 hom., cov: 33)

Exomes 𝑓: 0.12 ( 2454 hom. )

Consequence

MICD
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

23 publications found

Variant links:

Genes affected

MICD (HGNC:7093): (MHC class I polypeptide-related sequence D (pseudogene))

MICD links:

POLR1HASP (HGNC:):

POLR1HASP 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 (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29972595G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
POLR1HASP	ENST00000849678.1 link	n.589-25679C>T	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+4008C>T	intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1 link	n.506-15845C>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23113

AN:

152118

Hom.:

2075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.123

AC:

34491

AN:

281320

Hom.:

2454

AF XY:

0.123

AC XY:

17825

AN XY:

145068

show subpopulations

African (AFR)

AF:

0.208

AC:

1653

AN:

7944

American (AMR)

AF:

0.223

AC:

2324

AN:

10444

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

1239

AN:

9642

East Asian (EAS)

AF:

0.159

AC:

3753

AN:

23550

South Asian (SAS)

AF:

0.189

AC:

2164

AN:

11434

European-Finnish (FIN)

AF:

0.0900

AC:

2087

AN:

23190

Middle Eastern (MID)

AF:

0.112

AC:

155

AN:

1380

European-Non Finnish (NFE)

AF:

0.107

AC:

18760

AN:

176016

Other (OTH)

AF:

0.133

AC:

2356

AN:

17720

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1387

2773

4160

5546

6933

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

256

384

512

640

<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:

0.152

AC:

23165

AN:

152236

Hom.:

2086

Cov.:

AF XY:

0.151

AC XY:

11259

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.217

AC:

9002

AN:

41490

American (AMR)

AF:

0.216

AC:

3306

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

453

AN:

3470

East Asian (EAS)

AF:

0.124

AC:

645

AN:

5192

South Asian (SAS)

AF:

0.199

AC:

959

AN:

4828

European-Finnish (FIN)

AF:

0.0802

AC:

852

AN:

10618

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.110

AC:

7502

AN:

68010

Other (OTH)

AF:

0.168

AC:

356

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1008

2016

3024

4032

5040

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:

0.125

Hom.:

4380

Bravo

AF:

0.166

Asia WGS

AF:

0.157

AC:

546

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

6.6

(source)

DANN

Benign

0.56

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over