Variant rs4791362 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001310219.2(GSG1L2):c.311-151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 631,666 control chromosomes in the GnomAD database, including 18,041 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 0.22 ( 3951 hom., cov: 32)

Exomes 𝑓: 0.23 ( 14090 hom. )

Consequence

GSG1L2
NM_001310219.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.310

Variant links:

Genes affected

GSG1L2 (HGNC:51826): (GSG1 like 2) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

GSG1L2 links:

ENSG00000283025 (HGNC:):

ENSG00000283025 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L2	NM_001310219.2 link	c.311-151C>T		intron_variant		ENST00000399363.5	NP_001297148.1	A8MUP6
LOC124903925	XR_007065616.1 link	n.2420G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSG1L2	ENST00000399363.5 link	c.311-151C>T		intron_variant		5	NM_001310219.2	ENSP00000465978.1		A8MUP6
ENSG00000283025	ENST00000635215.1 link	n.2606G>A		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33640

AN:

151876

Hom.:

3949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.215

GnomAD4 exome

AF:

0.229

AC:

109934

AN:

479672

Hom.:

14090

Cov.:

AF XY:

0.233

AC XY:

59510

AN XY:

255712

show subpopulations

Gnomad4 AFR exome

AF:

0.221

Gnomad4 AMR exome

AF:

0.351

Gnomad4 ASJ exome

AF:

0.176

Gnomad4 EAS exome

AF:

0.384

Gnomad4 SAS exome

AF:

0.322

Gnomad4 FIN exome

AF:

0.289

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.218

GnomAD4 genome

AF:

0.222

AC:

33667

AN:

151994

Hom.:

3951

Cov.:

AF XY:

0.230

AC XY:

17049

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.225

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.368

Gnomad4 SAS

AF:

0.325

Gnomad4 FIN

AF:

0.304

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.216

Alfa

AF:

0.196

Hom.:

4290

Bravo

AF:

0.223

Asia WGS

AF:

0.358

AC:

1244

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.8

DANN

Benign

0.55

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over