Genetic Variant MICD:n.29972973C>A (chr6-29972973-C-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 0.547 in 152,050 control chromosomes in the GnomAD database, including 23,186 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 0.55 ( 23186 hom., cov: 32)

Consequence

MICD
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

29 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29972973C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
POLR1HASP	ENST00000849678.1 link	n.589-26057G>T	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+3630G>T	intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1 link	n.506-16223G>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.547

AC:

83098

AN:

151932

Hom.:

23183

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.719

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.445

Gnomad EAS

AF:

0.563

Gnomad SAS

AF:

0.476

Gnomad FIN

AF:

0.690

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.512

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

GnomAD4 genome

AF:

0.547

AC:

83114

AN:

152050

Hom.:

23186

Cov.:

AF XY:

0.547

AC XY:

40652

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.459

AC:

19013

AN:

41444

American (AMR)

AF:

0.510

AC:

7785

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.445

AC:

1544

AN:

3470

East Asian (EAS)

AF:

0.563

AC:

2911

AN:

5170

South Asian (SAS)

AF:

0.472

AC:

2277

AN:

4820

European-Finnish (FIN)

AF:

0.690

AC:

7306

AN:

10588

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.594

AC:

40379

AN:

67974

Other (OTH)

AF:

0.517

AC:

1091

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1924

3848

5771

7695

9619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.574

Hom.:

74388

Bravo

AF:

0.533

Asia WGS

AF:

0.556

AC:

1935

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.5

(source)

DANN

Benign

0.57

PhyloP100

-1.0

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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