Genetic Variant MICA-AS1:n.568-1146A>G (chr6-31384336-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 ENST00000745027.1(MICA-AS1):n.568-1146A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,756 control chromosomes in the GnomAD database, including 2,850 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 0.18 ( 2850 hom., cov: 30)

Consequence

MICA-AS1
ENST00000745027.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

Publications

35 publications found

Variant links:

Genes affected

MICA-AS1 (HGNC:):

MICA-AS1 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 (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MICA-AS1	ENST00000745027.1 link	n.568-1146A>G	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1 link	n.331-1146A>G	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745029.1 link	n.232+576A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27688

AN:

151638

Hom.:

2847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.0889

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.0998

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.217

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

GnomAD4 genome

AF:

0.183

AC:

27715

AN:

151756

Hom.:

2850

Cov.:

AF XY:

0.179

AC XY:

13243

AN XY:

74180

show subpopulations

African (AFR)

AF:

0.180

AC:

7448

AN:

41348

American (AMR)

AF:

0.251

AC:

3828

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

398

AN:

3466

East Asian (EAS)

AF:

0.0895

AC:

461

AN:

5152

South Asian (SAS)

AF:

0.206

AC:

990

AN:

4800

European-Finnish (FIN)

AF:

0.0998

AC:

1055

AN:

10574

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12864

AN:

67862

Other (OTH)

AF:

0.215

AC:

453

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1091

2182

3272

4363

5454

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.184

Hom.:

7032

Bravo

AF:

0.196

Asia WGS

AF:

0.185

AC:

644

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

8.3

(source)

DANN

Benign

0.58

PhyloP100

0.19

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