NM_001109763.2:c.397+16352C>T

Variant names:

• chr16-27946804-G-A
• rs7193224
• NM_001109763.2:c.397+16352C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001109763.2(GSG1L):​c.397+16352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,004 control chromosomes in the GnomAD database, including 4,900 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 0.23 (4900 hom., cov: 31)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.397+16352C>T		intron_variant	Intron 2 of 6	ENST00000447459.7	NP_001103233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSG1L	ENST00000447459.7	c.397+16352C>T		intron_variant	Intron 2 of 6	2	NM_001109763.2	ENSP00000394954.2
GSG1L	ENST00000395724.7	c.397+16352C>T		intron_variant	Intron 2 of 5	1		ENSP00000379074.3
GSG1L	ENST00000562611.1	n.160+16352C>T		intron_variant	Intron 2 of 6	3		ENSP00000454942.1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35563 AN: 151886 Hom.: 4890 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.234 AC: 35608 AN: 152004 Hom.: 4900 Cov.: 31 AF XY: 0.235 AC XY: 17452 AN XY: 74278

African (AFR) AF: 0.377 AC: 15616 AN: 41428

American (AMR) AF: 0.215 AC: 3288 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 894 AN: 3472

East Asian (EAS) AF: 0.132 AC: 682 AN: 5168

South Asian (SAS) AF: 0.302 AC: 1452 AN: 4808

European-Finnish (FIN) AF: 0.158 AC: 1668 AN: 10566

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11321 AN: 67988

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.190 Hom.: 8809

Bravo AF: 0.244

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		1.6
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: rs7193224; hg19: chr16-27958125;