rs1010060

Positions:

• chr16-27934717-G-A

Variant summary

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

The NM_001109763.2(GSG1L):​c.397+28439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 152,138 control chromosomes in the GnomAD database, including 386 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 0.057 (386 hom., cov: 32)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSG1L	NM_001109763.2	c.397+28439C>T		intron_variant		ENST00000447459.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSG1L	ENST00000447459.7	c.397+28439C>T		intron_variant		2	NM_001109763.2	P1
GSG1L	ENST00000395724.7	c.397+28439C>T		intron_variant		1
GSG1L	ENST00000562611.1	c.161+28439C>T		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8611 AN: 152020 Hom.: 383 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0567 AC: 8620 AN: 152138 Hom.: 386 Cov.: 32 AF XY: 0.0582 AC XY: 4331 AN XY: 74372

Gnomad4 AFR AF: 0.0200

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0769

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0526

Gnomad4 OTH AF: 0.0849

Alfa AF: 0.0647 Hom.: 135

Bravo AF: 0.0670

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.054
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010060; hg19: chr16-27946038; COSMIC: COSV66592432;