Genetic Variant MICA-AS1:n.568-1073A>G (chr6-31384263-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.568-1073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,858 control chromosomes in the GnomAD database, including 4,644 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 0.23 ( 4644 hom., cov: 31)

Consequence

MICA-AS1
ENST00000745027.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

Publications

23 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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.568-1073A>G	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1 link	n.331-1073A>G	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745029.1 link	n.232+649A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35664

AN:

151740

Hom.:

4646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.218

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.286

Gnomad OTH

AF:

0.220

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

GnomAD4 genome

AF:

0.235

AC:

35674

AN:

151858

Hom.:

4644

Cov.:

AF XY:

0.230

AC XY:

17090

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.142

AC:

5864

AN:

41432

American (AMR)

AF:

0.225

AC:

3436

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

1382

AN:

3460

East Asian (EAS)

AF:

0.217

AC:

1122

AN:

5166

South Asian (SAS)

AF:

0.160

AC:

772

AN:

4814

European-Finnish (FIN)

AF:

0.271

AC:

2860

AN:

10558

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.286

AC:

19415

AN:

67868

Other (OTH)

AF:

0.218

AC:

458

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1329

2658

3988

5317

6646

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.276

Hom.:

19219

Bravo

AF:

0.230

Asia WGS

AF:

0.187

AC:

652

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.5

(source)

DANN

Benign

0.77

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