rs1645336

Positions:

• chr16-27818353-T-C
• chr16-27818353-T-G

Variant summary

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

The NM_001109763.2(GSG1L):​c.830+10436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,978 control chromosomes in the GnomAD database, including 10,116 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 0.34 (10116 hom., cov: 32)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

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 (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.830+10436A>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.830+10436A>G		intron_variant		2	NM_001109763.2	ENSP00000394954.2
GSG1L	ENST00000395724.7	c.677+10436A>G		intron_variant		1		ENSP00000379074.3
GSG1L	ENST00000569166.1	c.419+5509A>G		intron_variant		1		ENSP00000454880.1
GSG1L	ENST00000380897.7	c.365+10436A>G		intron_variant		1		ENSP00000370282.3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51501 AN: 151860 Hom.: 10089 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.339 AC: 51570 AN: 151978 Hom.: 10116 Cov.: 32 AF XY: 0.337 AC XY: 25070 AN XY: 74310

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.308

Alfa AF: 0.257 Hom.: 6623

Bravo AF: 0.366

Asia WGS AF: 0.359 AC: 1251 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	1.1
DANN	Benign	0.19

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: rs1645336; hg19: chr16-27829674;