16-27839299-C-T

Position:

• chr16-27839299-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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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=-0.94).
• 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
GSG1L	NM_001109763.2	c.662+5651G>A		intron_variant		ENST00000447459.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSG1L	ENST00000447459.7	c.662+5651G>A		intron_variant		2	NM_001109763.2	P1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39425 AN: 152042 Hom.: 5511 Cov.: 32

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

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

Other links and lift over

dbSNP: rs1072594; hg19: chr16-27850620;