16-27839299-C-T

Variant names:

• chr16-27839299-C-T
• rs1072594
• NM_001109763.2:c.662+5651G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001109763.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSG1L	NM_001109763.2	MANE Select	c.662+5651G>A		intron	N/A	NP_001103233.1	Q6UXU4-1
	GSG1L	NM_001323900.2		c.662+5651G>A		intron	N/A	NP_001310829.1
	GSG1L	NM_001323901.2		c.509+5651G>A		intron	N/A	NP_001310830.1	Q6UXU4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSG1L	ENST00000447459.7	TSL:2 MANE Select	c.662+5651G>A		intron	N/A	ENSP00000394954.2	Q6UXU4-1
	GSG1L	ENST00000395724.7	TSL:1	c.509+5651G>A		intron	N/A	ENSP00000379074.3	Q6UXU4-3
	GSG1L	ENST00000569166.1	TSL:1	c.197+5651G>A		intron	N/A	ENSP00000454880.1	Q6UXU4-4

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

African (AFR) AF: 0.186 AC: 7707 AN: 41520

American (AMR) AF: 0.399 AC: 6098 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1907 AN: 5166

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2799 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18118 AN: 67994

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.266 Hom.: 18222

Bravo AF: 0.269

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.018
DANN	Benign	0.31
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1072594; hg19: chr16-27850620;