GeneBe

rs12621103

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000409011.5(GEMIN6):​c.-477T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GEMIN6
ENST00000409011.5 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

3 publications found
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]
SRSF7 (HGNC:10789): (serine and arginine rich splicing factor 7) The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an N-terminal RNA recognition motif (RRM) for binding RNA and a C-terminal RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2018]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409011.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SRSF7
NM_001363802.1
c.-366A>T
upstream_gene
N/ANP_001350731.1C9JAB2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GEMIN6
ENST00000409011.5
TSL:1
c.-477T>A
5_prime_UTR
Exon 1 of 6ENSP00000387191.1B9A037
SRSF7
ENST00000446327.6
TSL:2
c.-366A>T
upstream_gene
N/AENSP00000402264.2Q16629-4
SRSF7
ENST00000425778.5
TSL:2
n.-366A>T
upstream_gene
N/AENSP00000400246.1A0A0B4J1Z1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
163318
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
87212
African (AFR)
AF:
0.00
AC:
0
AN:
5536
American (AMR)
AF:
0.00
AC:
0
AN:
8976
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
4258
East Asian (EAS)
AF:
0.00
AC:
0
AN:
8360
South Asian (SAS)
AF:
0.00
AC:
0
AN:
26818
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
7696
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
612
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
92364
Other (OTH)
AF:
0.00
AC:
0
AN:
8698
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.52
CADD
Benign
5.6
DANN
Benign
0.86
PhyloP100
-0.29
PromoterAI
-0.013
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs12621103; hg19: chr2-38978764; API