Genetic Variant MICD:n.29974306C>T (chr6-29974306-C-T) – 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 0.263 in 151,142 control chromosomes in the GnomAD database, including 5,497 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 0.26 ( 5497 hom., cov: 28)

Consequence

MICD
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Publications

41 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29974306C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
POLR1HASP	ENST00000849678.1 link	n.589-27390G>A	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+2297G>A	intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1 link	n.506-17556G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39701

AN:

151024

Hom.:

5497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.263

AC:

39697

AN:

151142

Hom.:

5497

Cov.:

AF XY:

0.263

AC XY:

19355

AN XY:

73722

show subpopulations

African (AFR)

AF:

0.200

AC:

8231

AN:

41124

American (AMR)

AF:

0.252

AC:

3823

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

650

AN:

3470

East Asian (EAS)

AF:

0.311

AC:

1593

AN:

5116

South Asian (SAS)

AF:

0.170

AC:

808

AN:

4756

European-Finnish (FIN)

AF:

0.364

AC:

3782

AN:

10382

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.295

AC:

19982

AN:

67796

Other (OTH)

AF:

0.236

AC:

497

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1425

2850

4274

5699

7124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.277

Hom.:

23827

Bravo

AF:

0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

-0.16

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