dbSNP rs2596565: MICA-AS1:n.568-2362C>T (chr6-31385552-G-A) – 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.568-2362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 152,138 control chromosomes in the GnomAD database, including 589 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 0.076 ( 589 hom., cov: 32)

Consequence

MICA-AS1
ENST00000745027.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.197

Publications

35 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901300	XR_007059542.1 link	n.74+222G>A		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.568-2362C>T		intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1 link	n.330+1290C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0757

AC:

11509

AN:

152020

Hom.:

589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0355

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.0362

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.00481

Gnomad SAS

AF:

0.0607

Gnomad FIN

AF:

0.0777

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0546

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

GnomAD4 genome

AF:

0.0757

AC:

11513

AN:

152138

Hom.:

589

Cov.:

AF XY:

0.0713

AC XY:

5304

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0355

AC:

1472

AN:

41474

American (AMR)

AF:

0.0361

AC:

552

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0455

AC:

158

AN:

3470

East Asian (EAS)

AF:

0.00463

AC:

AN:

5182

South Asian (SAS)

AF:

0.0618

AC:

298

AN:

4820

European-Finnish (FIN)

AF:

0.0777

AC:

824

AN:

10600

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7928

AN:

67998

Other (OTH)

AF:

0.0540

AC:

114

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

538

1076

1613

2151

2689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.111

Hom.:

2376

Bravo

AF:

0.0697

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.3

(source)

DANN

Benign

0.58

PhyloP100

0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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