Genetic Variant MICD:n.29972108G>T (chr6-29972108-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MICD
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.203

Publications

5 publications found

Variant links:

Genes affected

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

MICD links:

POLR1HASP (HGNC:):

POLR1HASP links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29972108G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MICD	ENST00000413248.1 link	n.256+101C>A	intron_variant	Intron 1 of 2	6
POLR1HASP	ENST00000849678.1 link	n.589-25192C>A	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+4495C>A	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

240580

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

124810

African (AFR)

AF:

0.00

AC:

AN:

7424

American (AMR)

AF:

0.00

AC:

AN:

11632

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

7904

East Asian (EAS)

AF:

0.00

AC:

AN:

17846

South Asian (SAS)

AF:

0.00

AC:

AN:

17508

European-Finnish (FIN)

AF:

0.00

AC:

AN:

15116

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1178

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

147044

Other (OTH)

AF:

0.00

AC:

AN:

14928

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.070

(source)

DANN

Benign

0.50

PhyloP100

-0.20

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over