dbSNP rs13437082: MICA-AS1:n.568-3593G>A (chr6-31386783-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.568-3593G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,940 control chromosomes in the GnomAD database, including 8,087 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 0.32 ( 8087 hom., cov: 31)

Consequence

MICA-AS1
ENST00000745027.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

57 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901300	XR_007059542.1 link	n.75-480C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICA-AS1	ENST00000745027.1 link	n.568-3593G>A		intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1 link	n.330+59G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48202

AN:

151822

Hom.:

8073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.472

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.565

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.339

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.331

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

GnomAD4 genome

AF:

0.318

AC:

48263

AN:

151940

Hom.:

8087

Cov.:

AF XY:

0.322

AC XY:

23948

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.376

AC:

15562

AN:

41412

American (AMR)

AF:

0.374

AC:

5716

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.565

AC:

1961

AN:

3470

East Asian (EAS)

AF:

0.327

AC:

1690

AN:

5172

South Asian (SAS)

AF:

0.309

AC:

1488

AN:

4812

European-Finnish (FIN)

AF:

0.339

AC:

3574

AN:

10546

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.251

AC:

17032

AN:

67958

Other (OTH)

AF:

0.337

AC:

708

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1647

3294

4941

6588

8235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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.:

26630

Bravo

AF:

0.324

Asia WGS

AF:

0.329

AC:

1143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.9

(source)

DANN

Benign

0.54

PhyloP100

-1.2

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