Genetic Variant MICA-AS1:n.831G>A (chr6-31382927-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 ENST00000745027.1(MICA-AS1):n.831G>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 0.749 in 152,104 control chromosomes in the GnomAD database, including 43,077 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 0.75 ( 43077 hom., cov: 31)

Consequence

MICA-AS1
ENST00000745027.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.54

Publications

44 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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.831G>A	non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	ENST00000745028.1 link	n.594G>A	non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	ENST00000745029.1 link	n.496G>A	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113840

AN:

151984

Hom.:

43032

Cov.:

show subpopulations

Gnomad AFR

AF:

0.677

Gnomad AMI

AF:

0.896

Gnomad AMR

AF:

0.766

Gnomad ASJ

AF:

0.858

Gnomad EAS

AF:

0.925

Gnomad SAS

AF:

0.838

Gnomad FIN

AF:

0.832

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.749

Gnomad OTH

AF:

0.734

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

GnomAD4 genome

AF:

0.749

AC:

113936

AN:

152104

Hom.:

43077

Cov.:

AF XY:

0.756

AC XY:

56248

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.677

AC:

28062

AN:

41446

American (AMR)

AF:

0.767

AC:

11726

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.858

AC:

2976

AN:

3468

East Asian (EAS)

AF:

0.925

AC:

4777

AN:

5166

South Asian (SAS)

AF:

0.839

AC:

4041

AN:

4816

European-Finnish (FIN)

AF:

0.832

AC:

8813

AN:

10598

Middle Eastern (MID)

AF:

0.799

AC:

235

AN:

294

European-Non Finnish (NFE)

AF:

0.749

AC:

50925

AN:

67998

Other (OTH)

AF:

0.739

AC:

1564

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1413

2825

4238

5650

7063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<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:

0.751

Hom.:

126152

Bravo

AF:

0.735

Asia WGS

AF:

0.866

AC:

3013

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.3

(source)

DANN

Benign

0.51

PhyloP100

-2.5

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