rs713547

Positions:

• chr16-27820768-C-T

Variant summary

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

The NM_001109763.2(GSG1L):​c.830+8021G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,020 control chromosomes in the GnomAD database, including 4,038 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 0.21 (4038 hom., cov: 31)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.830+8021G>A		intron_variant		ENST00000447459.7	NP_001103233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSG1L	ENST00000447459.7	c.830+8021G>A		intron_variant		2	NM_001109763.2	ENSP00000394954	P1
GSG1L	ENST00000380897.7	c.365+8021G>A		intron_variant		1		ENSP00000370282
GSG1L	ENST00000395724.7	c.677+8021G>A		intron_variant		1		ENSP00000379074
GSG1L	ENST00000569166.1	c.419+3094G>A		intron_variant		1		ENSP00000454880

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32140 AN: 151902 Hom.: 4030 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.212 AC: 32178 AN: 152020 Hom.: 4038 Cov.: 31 AF XY: 0.212 AC XY: 15733 AN XY: 74314

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.210

Alfa AF: 0.154 Hom.: 3250

Bravo AF: 0.234

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs713547; hg19: chr16-27832089;