rs205391

Variant names:

• chr16-28041642-T-C
• rs205391
• NM_001109763.2:c.349+21434A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-28041642-T-C
• chr16-28041642-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.349+21434A>G		intron_variant	Intron 1 of 6	ENST00000447459.7	NP_001103233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSG1L	ENST00000447459.7	c.349+21434A>G		intron_variant	Intron 1 of 6	2	NM_001109763.2	ENSP00000394954.2
GSG1L	ENST00000395724.7	c.349+21434A>G		intron_variant	Intron 1 of 5	1		ENSP00000379074.3
GSG1L	ENST00000562611.1	n.112+21434A>G		intron_variant	Intron 1 of 6	3		ENSP00000454942.1

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

African (AFR) AF: 0.851 AC: 35320 AN: 41484

American (AMR) AF: 0.897 AC: 13723 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2962 AN: 3470

East Asian (EAS) AF: 0.832 AC: 4308 AN: 5180

South Asian (SAS) AF: 0.873 AC: 4214 AN: 4828

European-Finnish (FIN) AF: 0.803 AC: 8499 AN: 10580

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56424 AN: 68010

Other (OTH) AF: 0.856 AC: 1811 AN: 2116

Alfa AF: 0.835 Hom.: 192996

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
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs205391; hg19: chr16-28052963;