Genetic Variant MICA-AS1:n.963G>A (chr6-31394533-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000606743.1(MICA-AS1):n.963G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 147,466 control chromosomes in the GnomAD database, including 1,106 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 0.10 ( 1105 hom., cov: 31)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

MICA-AS1
ENST00000606743.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.03

Publications

17 publications found

Variant links:

Genes affected

MICA-AS1 (HGNC:):

MICA-AS1 links:

MICA-AS1 (HGNC:53631): (MICA antisense RNA 1)

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICA-AS1	NR_148222.1 link	n.1102G>A		non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	NR_148223.1 link	n.1135G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MICA-AS1	ENST00000606743.1 link	n.963G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
MICA-AS1	ENST00000745010.1 link	n.1425G>A	non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	ENST00000745011.1 link	n.1362G>A	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15295

AN:

147318

Hom.:

1102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.0270

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0764

Gnomad EAS

AF:

0.0275

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.00777

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0798

Gnomad OTH

AF:

0.147

GnomAD4 exome

AF:

0.133

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.104

AC:

15311

AN:

147436

Hom.:

1105

Cov.:

AF XY:

0.101

AC XY:

7230

AN XY:

71908

show subpopulations

African (AFR)

AF:

0.167

AC:

6561

AN:

39274

American (AMR)

AF:

0.144

AC:

2074

AN:

14412

Ashkenazi Jewish (ASJ)

AF:

0.0764

AC:

251

AN:

3284

East Asian (EAS)

AF:

0.0278

AC:

139

AN:

5006

South Asian (SAS)

AF:

0.103

AC:

475

AN:

4614

European-Finnish (FIN)

AF:

0.00777

AC:

AN:

10290

Middle Eastern (MID)

AF:

0.132

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.0798

AC:

5373

AN:

67328

Other (OTH)

AF:

0.144

AC:

297

AN:

2060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

659

1317

1976

2634

3293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.0851

Hom.:

114

Bravo

AF:

0.118

Asia WGS

AF:

0.0700

AC:

241

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.6

(source)

DANN

Benign

0.34

PhyloP100

-3.0

Mutation Taster

=99/1

polymorphism

(source)

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