rs205370

Positions:

• chr16-28011108-A-G

Variant summary

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

The NM_001109763.2(GSG1L):​c.350-47905T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,044 control chromosomes in the GnomAD database, including 3,912 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 (3912 hom., cov: 32)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.350-47905T>C		intron_variant		ENST00000447459.7	NP_001103233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSG1L	ENST00000447459.7	c.350-47905T>C		intron_variant		2	NM_001109763.2	ENSP00000394954.2
GSG1L	ENST00000395724.7	c.350-47905T>C		intron_variant		1		ENSP00000379074.3
GSG1L	ENST00000562611.1	n.113-47905T>C		intron_variant		3		ENSP00000454942.1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32653 AN: 151926 Hom.: 3915 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.215 AC: 32668 AN: 152044 Hom.: 3912 Cov.: 32 AF XY: 0.220 AC XY: 16325 AN XY: 74326

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.225

Alfa AF: 0.236 Hom.: 3657

Bravo AF: 0.212

Asia WGS AF: 0.384 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205370; hg19: chr16-28022429;