Variant rs1056104 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024775.10(GEMIN6):c.419G>A(p.Gly140Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0827 in 1,613,982 control chromosomes in the GnomAD database, including 7,472 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.070 ( 575 hom., cov: 31)

Exomes 𝑓: 0.084 ( 6897 hom. )

Consequence

GEMIN6
NM_024775.10 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.05

Variant links:

Genes affected

GEMIN6 (HGNC:20044): (gem nuclear organelle associated protein 6) GEMIN6 is part of a large macromolecular complex, localized to both the cytoplasm and the nucleus, that plays a role in the cytoplasmic assembly of small nuclear ribonucleoproteins (snRNPs). Other members of this complex include SMN (MIM 600354), GEMIN2 (SIP1; MIM 602595), GEMIN3 (DDX20; MIM 606168), GEMIN4 (MIM 606969), and GEMIN5 (MIM 607005).[supplied by OMIM, Jul 2002]

GEMIN6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015923977).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GEMIN6	NM_024775.10 linkuse as main transcript	c.419G>A	p.Gly140Asp	missense_variant	3/3	ENST00000281950.8	NP_079051.9	Q8WXD5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GEMIN6	ENST00000281950.8 linkuse as main transcript	c.419G>A	p.Gly140Asp	missense_variant	3/3	1	NM_024775.10	ENSP00000281950.2	Q8WXD5
GEMIN6	ENST00000409011.5 linkuse as main transcript	c.*277G>A		3_prime_UTR_variant	6/6	1		ENSP00000387191.1	B9A037
GEMIN6	ENST00000409566.1 linkuse as main transcript	c.*267G>A		3_prime_UTR_variant	4/4	2		ENSP00000386613.1	B8ZZ85

Frequencies

GnomAD3 genomes

AF:

0.0703

AC:

10685

AN:

152040

Hom.:

575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0146

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.0970

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.0513

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0748

Gnomad OTH

AF:

0.0761

GnomAD3 exomes

AF:

0.104

AC:

26112

AN:

251324

Hom.:

1928

AF XY:

0.106

AC XY:

14398

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.0129

Gnomad AMR exome

AF:

0.123

Gnomad ASJ exome

AF:

0.114

Gnomad EAS exome

AF:

0.295

Gnomad SAS exome

AF:

0.153

Gnomad FIN exome

AF:

0.0537

Gnomad NFE exome

AF:

0.0755

Gnomad OTH exome

AF:

0.105

GnomAD4 exome

AF:

0.0840

AC:

122740

AN:

1461824

Hom.:

6897

Cov.:

AF XY:

0.0858

AC XY:

62430

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.0124

Gnomad4 AMR exome

AF:

0.120

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.316

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.0535

Gnomad4 NFE exome

AF:

0.0715

Gnomad4 OTH exome

AF:

0.0914

GnomAD4 genome

AF:

0.0702

AC:

10686

AN:

152158

Hom.:

575

Cov.:

AF XY:

0.0744

AC XY:

5538

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0147

Gnomad4 AMR

AF:

0.0975

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.289

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.0513

Gnomad4 NFE

AF:

0.0747

Gnomad4 OTH

AF:

0.0749

Alfa

AF:

0.0787

Hom.:

1358

Bravo

AF:

0.0711

TwinsUK

AF:

0.0707

AC:

262

ALSPAC

AF:

0.0734

AC:

283

ESP6500AA

AF:

0.0182

AC:

ESP6500EA

AF:

0.0777

AC:

668

ExAC

AF:

0.103

AC:

12462

Asia WGS

AF:

0.184

AC:

639

AN:

3478

EpiCase

AF:

0.0818

EpiControl

AF:

0.0857

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.046

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.32

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.63

MetaRNN

Benign

0.0016

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

PrimateAI

Uncertain

0.62

PROVEAN

Benign

-1.1

REVEL

Benign

0.078

Sift

Benign

0.16

Sift4G

Benign

0.33

Polyphen

0.029

Vest4

0.13

MPC

0.0031

ClinPred

0.032

GERP RS

4.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.042

gMVP

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over