16-28061349-G-C

Position:

• chr16-28061349-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001109763.2(GSG1L):​c.349+1727C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,096 control chromosomes in the GnomAD database, including 45,364 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 0.77 (45364 hom., cov: 31)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.349+1727C>G		intron_variant		ENST00000447459.7	NP_001103233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSG1L	ENST00000447459.7	c.349+1727C>G		intron_variant		2	NM_001109763.2	ENSP00000394954	P1
GSG1L	ENST00000395724.7	c.349+1727C>G		intron_variant		1		ENSP00000379074
GSG1L	ENST00000562611.1	c.113+1727C>G		intron_variant, NMD_transcript_variant		3		ENSP00000454942

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117140 AN: 151978 Hom.: 45318 Cov.: 31

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.771 AC: 117246 AN: 152096 Hom.: 45364 Cov.: 31 AF XY: 0.774 AC XY: 57506 AN XY: 74334

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.751

Alfa AF: 0.740 Hom.: 4889

Bravo AF: 0.776

Asia WGS AF: 0.860 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205418; hg19: chr16-28072670;