dbSNP rs12524487: MICA-AS1:n.568-3271G>A (chr6-31386461-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.568-3271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,210 control chromosomes in the GnomAD database, including 457 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 0.062 ( 457 hom., cov: 32)

Consequence

MICA-AS1
ENST00000745027.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.167

Publications

24 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 = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901300	XR_007059542.1 link	n.75-802C>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.568-3271G>A		intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1 link	n.330+381G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0617

AC:

9378

AN:

152092

Hom.:

457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0136

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.0629

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.0844

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0711

Gnomad OTH

AF:

0.0521

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

GnomAD4 genome

AF:

0.0616

AC:

9374

AN:

152210

Hom.:

457

Cov.:

AF XY:

0.0653

AC XY:

4862

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0135

AC:

563

AN:

41552

American (AMR)

AF:

0.0504

AC:

770

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0629

AC:

218

AN:

3468

East Asian (EAS)

AF:

0.223

AC:

1157

AN:

5180

South Asian (SAS)

AF:

0.0842

AC:

406

AN:

4820

European-Finnish (FIN)

AF:

0.123

AC:

1300

AN:

10592

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0711

AC:

4837

AN:

67988

Other (OTH)

AF:

0.0511

AC:

108

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

439

878

1318

1757

2196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0761

Hom.:

1276

Bravo

AF:

0.0548

Asia WGS

AF:

0.0910

AC:

318

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

3.1

(source)

DANN

Benign

0.30

PhyloP100

0.17

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