dbSNP rs4791362: GSG1L2:c.311-151C>T (chr17-9810769-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GSG1L2	NM_001310219.2 link	c.311-151C>T		intron_variant	Intron 1 of 4	ENST00000399363.5	NP_001297148.1	A8MUP6
LOC124903925	XR_007065616.1 link	n.2420G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSG1L2	ENST00000399363.5 link	c.311-151C>T		intron_variant	Intron 1 of 4	5	NM_001310219.2	ENSP00000465978.1		A8MUP6
ENSG00000283025	ENST00000635215.1 link	n.2606G>A		non_coding_transcript_exon_variant	Exon 3 of 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

African (AFR)

AF:

0.221

AC:

3005

AN:

13600

American (AMR)

AF:

0.351

AC:

8870

AN:

25264

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

2667

AN:

15130

East Asian (EAS)

AF:

0.384

AC:

12113

AN:

31510

South Asian (SAS)

AF:

0.322

AC:

15833

AN:

49112

European-Finnish (FIN)

AF:

0.289

AC:

8828

AN:

30548

Middle Eastern (MID)

AF:

0.178

AC:

389

AN:

2190

European-Non Finnish (NFE)

AF:

0.183

AC:

52249

AN:

284908

Other (OTH)

AF:

0.218

AC:

5980

AN:

27410

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

4028

8055

12083

16110

20138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

444

888

1332

1776

2220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.222

AC:

33667

AN:

151994

Hom.:

3951

Cov.:

AF XY:

0.230

AC XY:

17049

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.225

AC:

9311

AN:

41456

American (AMR)

AF:

0.283

AC:

4329

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

593

AN:

3470

East Asian (EAS)

AF:

0.368

AC:

1895

AN:

5156

South Asian (SAS)

AF:

0.325

AC:

1562

AN:

4808

European-Finnish (FIN)

AF:

0.304

AC:

3201

AN:

10530

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.178

AC:

12105

AN:

67980

Other (OTH)

AF:

0.216

AC:

457

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1315

2630

3945

5260

6575

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.198

Hom.:

5566

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

(source)

DANN

Benign

0.55

PhyloP100

0.31

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over