chr16-28041642-T-C

Position:

• chr16-28041642-T-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+21434A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,170 control chromosomes in the GnomAD database, including 54,152 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 0.84 (54152 hom., cov: 30)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.349+21434A>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+21434A>G		intron_variant		2	NM_001109763.2	ENSP00000394954	P1
GSG1L	ENST00000395724.7	c.349+21434A>G		intron_variant		1		ENSP00000379074
GSG1L	ENST00000562611.1	c.113+21434A>G		intron_variant, NMD_transcript_variant		3		ENSP00000454942

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128195 AN: 152050 Hom.: 54091 Cov.: 30

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.843 AC: 128318 AN: 152170 Hom.: 54152 Cov.: 30 AF XY: 0.844 AC XY: 62819 AN XY: 74410

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.854

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.856

Alfa AF: 0.833 Hom.: 82041

Bravo AF: 0.849

Asia WGS AF: 0.878 AC: 3054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205391; hg19: chr16-28052963;