dbSNP rs2844533: MICA-AS1:n.733C>T (chr6-31383025-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.733C>T 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 152,028 control chromosomes in the GnomAD database, including 43,055 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 ( 43055 hom., cov: 31)

Consequence

MICA-AS1
ENST00000745027.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Publications

35 publications found

Variant links:

COSMIC-nc: COSV69645936

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=-0.74).

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.733C>T	non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	ENST00000745028.1 link	n.496C>T	non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	ENST00000745029.1 link	n.398C>T	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113779

AN:

151910

Hom.:

43011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.677

Gnomad AMI

AF:

0.896

Gnomad AMR

AF:

0.767

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:

0.735

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

GnomAD4 genome

AF:

0.749

AC:

113873

AN:

152028

Hom.:

43055

Cov.:

AF XY:

0.756

AC XY:

56216

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.677

AC:

28027

AN:

41426

American (AMR)

AF:

0.767

AC:

11719

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.858

AC:

2977

AN:

3470

East Asian (EAS)

AF:

0.925

AC:

4787

AN:

5174

South Asian (SAS)

AF:

0.839

AC:

4039

AN:

4816

European-Finnish (FIN)

AF:

0.832

AC:

8791

AN:

10570

Middle Eastern (MID)

AF:

0.799

AC:

235

AN:

294

European-Non Finnish (NFE)

AF:

0.749

AC:

50917

AN:

67978

Other (OTH)

AF:

0.740

AC:

1564

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1410

2820

4230

5640

7050

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:

0.755

Hom.:

172188

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

-0.74

CADD

Benign

6.5

(source)

DANN

Benign

0.88

PhyloP100

0.23

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