Genetic Variant MICA-AS1:n.568-1664T>C (chr6-31384854-A-G) – 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.568-1664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,468 control chromosomes in the GnomAD database, including 10,257 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 0.36 ( 10257 hom., cov: 32)

Consequence

MICA-AS1
ENST00000745027.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211

Publications

29 publications found

Variant links:

Genes affected

MICA-AS1 (HGNC:):

MICA-AS1 links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 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.568-1664T>C	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1 link	n.331-1664T>C	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745029.1 link	n.232+58T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54447

AN:

151346

Hom.:

10244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.390

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

GnomAD4 genome

AF:

0.360

AC:

54505

AN:

151468

Hom.:

10257

Cov.:

AF XY:

0.366

AC XY:

27069

AN XY:

74052

show subpopulations

African (AFR)

AF:

0.379

AC:

15632

AN:

41198

American (AMR)

AF:

0.424

AC:

6434

AN:

15192

Ashkenazi Jewish (ASJ)

AF:

0.605

AC:

2085

AN:

3446

East Asian (EAS)

AF:

0.320

AC:

1648

AN:

5158

South Asian (SAS)

AF:

0.416

AC:

1991

AN:

4790

European-Finnish (FIN)

AF:

0.400

AC:

4230

AN:

10564

Middle Eastern (MID)

AF:

0.445

AC:

129

AN:

290

European-Non Finnish (NFE)

AF:

0.311

AC:

21070

AN:

67830

Other (OTH)

AF:

0.393

AC:

822

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1783

3567

5350

7134

8917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.333

Hom.:

22434

Bravo

AF:

0.363

Asia WGS

AF:

0.349

AC:

1216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

0.21

Splicing

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

Publications

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chr6-31384854-A-G

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