Genetic Variant GS1-24F4.2:n.602-5062A>G (chr8-6880060-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000531701.2(GS1-24F4.2):n.602-5062A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,052 control chromosomes in the GnomAD database, including 7,146 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 0.30 ( 7146 hom., cov: 32)

Consequence

GS1-24F4.2
ENST00000531701.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Publications

6 publications found

Variant links:

Genes affected

GS1-24F4.2 (HGNC:):

GS1-24F4.2 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GS1-24F4.2	ENST00000531701.2 link	n.602-5062A>G	intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1 link	n.352-5062A>G	intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1 link	n.794-5062A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46220

AN:

151932

Hom.:

7144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.271

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.300

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

GnomAD4 genome

AF:

0.304

AC:

46253

AN:

152052

Hom.:

7146

Cov.:

AF XY:

0.300

AC XY:

22292

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.320

AC:

13258

AN:

41448

American (AMR)

AF:

0.337

AC:

5144

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

981

AN:

3472

East Asian (EAS)

AF:

0.155

AC:

803

AN:

5176

South Asian (SAS)

AF:

0.190

AC:

914

AN:

4818

European-Finnish (FIN)

AF:

0.288

AC:

3037

AN:

10552

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.311

AC:

21113

AN:

67982

Other (OTH)

AF:

0.301

AC:

635

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1664

3328

4993

6657

8321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.227

Hom.:

648

Bravo

AF:

0.313

Asia WGS

AF:

0.222

AC:

774

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.84

(source)

DANN

Benign

0.20

PhyloP100

-1.7

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over