dbSNP rs5009448: MICD:n.29972711T>C (chr6-29972711-T-C) – 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 0.735 in 152,132 control chromosomes in the GnomAD database, including 41,356 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 0.73 ( 41356 hom., cov: 32)

Consequence

MICD
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

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 (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29972711T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
POLR1HASP	ENST00000849678.1 link	n.589-25795A>G	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+3892A>G	intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1 link	n.506-15961A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.735

AC:

111712

AN:

152014

Hom.:

41315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.770

Gnomad AMI

AF:

0.767

Gnomad AMR

AF:

0.764

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.678

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.782

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.716

Gnomad OTH

AF:

0.717

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

GnomAD4 genome

AF:

0.735

AC:

111805

AN:

152132

Hom.:

41356

Cov.:

AF XY:

0.734

AC XY:

54619

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.770

AC:

31927

AN:

41478

American (AMR)

AF:

0.765

AC:

11693

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

2051

AN:

3468

East Asian (EAS)

AF:

0.678

AC:

3509

AN:

5174

South Asian (SAS)

AF:

0.667

AC:

3220

AN:

4824

European-Finnish (FIN)

AF:

0.782

AC:

8285

AN:

10592

Middle Eastern (MID)

AF:

0.690

AC:

203

AN:

294

European-Non Finnish (NFE)

AF:

0.716

AC:

48700

AN:

67986

Other (OTH)

AF:

0.719

AC:

1519

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1533

3065

4598

6130

7663

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.724

Hom.:

79199

Bravo

AF:

0.740

Asia WGS

AF:

0.724

AC:

2520

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

3.5

(source)

DANN

Benign

0.42

PhyloP100

-0.63

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.

rs5009448

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