NM_001109763.2:c.349+10449C>T

Variant names:

• chr16-28052627-G-A
• rs205409
• NM_001109763.2:c.349+10449C>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.349+10449C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,956 control chromosomes in the GnomAD database, including 24,253 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 0.56 (24253 hom., cov: 32)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.349+10449C>T		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+10449C>T		intron_variant	Intron 1 of 6	2	NM_001109763.2	ENSP00000394954.2
GSG1L	ENST00000395724.7	c.349+10449C>T		intron_variant	Intron 1 of 5	1		ENSP00000379074.3
GSG1L	ENST00000562611.1	n.112+10449C>T		intron_variant	Intron 1 of 6	3		ENSP00000454942.1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84916 AN: 151838 Hom.: 24223 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.559 AC: 85003 AN: 151956 Hom.: 24253 Cov.: 32 AF XY: 0.563 AC XY: 41814 AN XY: 74270

African (AFR) AF: 0.490 AC: 20320 AN: 41430

American (AMR) AF: 0.651 AC: 9950 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2187 AN: 3466

East Asian (EAS) AF: 0.507 AC: 2604 AN: 5132

South Asian (SAS) AF: 0.756 AC: 3639 AN: 4816

European-Finnish (FIN) AF: 0.554 AC: 5846 AN: 10552

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38422 AN: 67962

Other (OTH) AF: 0.565 AC: 1193 AN: 2112

Alfa AF: 0.568 Hom.: 96604

Bravo AF: 0.562

Asia WGS AF: 0.627 AC: 2181 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	0.014
DANN	Benign	0.34
PhyloP100		-2.1
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: rs205409; hg19: chr16-28063948;