dbSNP rs7541193: GEMIN2P1:n.153699771G>T (chr1-153699771-G-T) – 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 0.609 in 151,824 control chromosomes in the GnomAD database, including 28,982 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 0.61 ( 28982 hom., cov: 30)

Consequence

GEMIN2P1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.869

Publications

9 publications found

Variant links:

Genes affected

GEMIN2P1 (HGNC:49561): (gem nuclear organelle associated protein 2 pseudogene 1)

GEMIN2P1 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GEMIN2P1		n.153699771G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

92272

AN:

151704

Hom.:

28930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.736

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.688

Gnomad ASJ

AF:

0.443

Gnomad EAS

AF:

0.736

Gnomad SAS

AF:

0.620

Gnomad FIN

AF:

0.478

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.592

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

GnomAD4 genome

AF:

0.609

AC:

92388

AN:

151824

Hom.:

28982

Cov.:

AF XY:

0.609

AC XY:

45187

AN XY:

74184

show subpopulations

African (AFR)

AF:

0.736

AC:

30468

AN:

41394

American (AMR)

AF:

0.689

AC:

10501

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.443

AC:

1536

AN:

3470

East Asian (EAS)

AF:

0.737

AC:

3807

AN:

5166

South Asian (SAS)

AF:

0.620

AC:

2987

AN:

4814

European-Finnish (FIN)

AF:

0.478

AC:

5022

AN:

10500

Middle Eastern (MID)

AF:

0.599

AC:

176

AN:

294

European-Non Finnish (NFE)

AF:

0.535

AC:

36319

AN:

67934

Other (OTH)

AF:

0.590

AC:

1240

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1742

3485

5227

6970

8712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.562

Hom.:

18874

Bravo

AF:

0.630

Asia WGS

AF:

0.656

AC:

2283

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.30

(source)

DANN

Benign

0.30

PhyloP100

-0.87

Splicing

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

Publications

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rs7541193

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