dbSNP rs4713240: MICE:n.29742949A>G (chr6-29742949-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 variant allele was found at a frequency of 0.232 in 152,264 control chromosomes in the GnomAD database, including 4,137 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 0.23 ( 4137 hom., cov: 34)

Consequence

MICE
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.576

Publications

30 publications found

Variant links:

Genes affected

MICE (HGNC:7094): (MHC class I polypeptide-related sequence E (pseudogene))

MICE links:

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

HLA-F-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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MICE		n.29742949A>G	intragenic_variant
HLA-F-AS1	NR_026972.1 link	n.429-4063T>C	intron_variant	Intron 2 of 5
HLA-F-AS1	NR_026973.1 link	n.150+5951T>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HLA-F-AS1	ENST00000399247.6 link	n.429-4063T>C	intron_variant	Intron 2 of 5	6
HLA-F-AS1	ENST00000434086.2 link	n.354-4063T>C	intron_variant	Intron 1 of 3	6
HLA-F-AS1	ENST00000458236.1 link	n.349+2524T>C	intron_variant	Intron 2 of 5	6

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35294

AN:

152146

Hom.:

4127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.200

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

GnomAD4 genome

AF:

0.232

AC:

35327

AN:

152264

Hom.:

4137

Cov.:

AF XY:

0.233

AC XY:

17318

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.206

AC:

8574

AN:

41540

American (AMR)

AF:

0.202

AC:

3094

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

637

AN:

3472

East Asian (EAS)

AF:

0.374

AC:

1938

AN:

5178

South Asian (SAS)

AF:

0.182

AC:

878

AN:

4826

European-Finnish (FIN)

AF:

0.282

AC:

2989

AN:

10606

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.243

AC:

16500

AN:

68014

Other (OTH)

AF:

0.200

AC:

424

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1441

2882

4322

5763

7204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<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:

0.239

Hom.:

14617

Bravo

AF:

0.227

Asia WGS

AF:

0.236

AC:

817

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.2

(source)

DANN

Benign

0.90

PhyloP100

0.58

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