rs1645336

Variant names:

• chr16-27818353-T-C
• rs1645336
• NM_001109763.2:c.830+10436A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-27818353-T-C
• chr16-27818353-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.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
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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.830+10436A>G		intron	N/A	NP_001103233.1	Q6UXU4-1
	GSG1L	NM_001323900.2		c.884+5509A>G		intron	N/A	NP_001310829.1
	GSG1L	NM_001323901.2		c.677+10436A>G		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.830+10436A>G		intron	N/A	ENSP00000394954.2	Q6UXU4-1
	GSG1L	ENST00000395724.7	TSL:1	c.677+10436A>G		intron	N/A	ENSP00000379074.3	Q6UXU4-3
	GSG1L	ENST00000569166.1	TSL:1	c.419+5509A>G		intron	N/A	ENSP00000454880.1	Q6UXU4-4

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

African (AFR) AF: 0.515 AC: 21311 AN: 41418

American (AMR) AF: 0.453 AC: 6919 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1713 AN: 5168

South Asian (SAS) AF: 0.284 AC: 1363 AN: 4802

European-Finnish (FIN) AF: 0.222 AC: 2342 AN: 10560

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16334 AN: 67966

Other (OTH) AF: 0.308 AC: 651 AN: 2112

Alfa AF: 0.268 Hom.: 9068

Bravo AF: 0.366

Asia WGS AF: 0.359 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		0.065
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: rs1645336; hg19: chr16-27829674;