rs1072594

Variant summary

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

The NM_001109763.2(GSG1L):​c.662+5651G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,160 control chromosomes in the GnomAD database, including 5,518 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 0.26 ( 5518 hom., cov: 32)

Consequence

GSG1L
NM_001109763.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62
Variant links:
Genes affected
GSG1L (HGNC:28283): (GSG1 like) Predicted to be involved in regulation of AMPA receptor activity. Predicted to be located in postsynaptic density. Predicted to be active in Schaffer collateral - CA1 synapse; glutamatergic synapse; and plasma membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GSG1LNM_001109763.2 linkuse as main transcriptc.662+5651G>A intron_variant ENST00000447459.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GSG1LENST00000447459.7 linkuse as main transcriptc.662+5651G>A intron_variant 2 NM_001109763.2 P1Q6UXU4-1

Frequencies

GnomAD3 genomes
AF:
0.259
AC:
39425
AN:
152042
Hom.:
5511
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.186
Gnomad AMI
AF:
0.232
Gnomad AMR
AF:
0.398
Gnomad ASJ
AF:
0.271
Gnomad EAS
AF:
0.369
Gnomad SAS
AF:
0.217
Gnomad FIN
AF:
0.264
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.266
Gnomad OTH
AF:
0.257
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.259
AC:
39436
AN:
152160
Hom.:
5518
Cov.:
32
AF XY:
0.262
AC XY:
19466
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.186
Gnomad4 AMR
AF:
0.399
Gnomad4 ASJ
AF:
0.271
Gnomad4 EAS
AF:
0.369
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.264
Gnomad4 NFE
AF:
0.266
Gnomad4 OTH
AF:
0.258
Alfa
AF:
0.265
Hom.:
6615
Bravo
AF:
0.269
Asia WGS
AF:
0.307
AC:
1067
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.018
DANN
Benign
0.31

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.

Other links and lift over

dbSNP: rs1072594; hg19: chr16-27850620; API