Genetic Variant ENST00000531701.2:n.602-5000C>T (chr8-6880122-C-T) – 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.602-5000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,114 control chromosomes in the GnomAD database, including 2,815 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 0.17 ( 2815 hom., cov: 33)

Consequence

GS1-24F4.2
ENST00000531701.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.686

Publications

0 publications found

Variant links:

Genes affected

GS1-24F4.2 (HGNC:):

GS1-24F4.2 links:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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.602-5000C>T	intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1 link	n.352-5000C>T	intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1 link	n.794-5000C>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25247

AN:

151996

Hom.:

2809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0384

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.144

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

GnomAD4 genome

AF:

0.166

AC:

25253

AN:

152114

Hom.:

2815

Cov.:

AF XY:

0.174

AC XY:

12975

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0383

AC:

1591

AN:

41530

American (AMR)

AF:

0.206

AC:

3141

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

387

AN:

3470

East Asian (EAS)

AF:

0.388

AC:

2010

AN:

5176

South Asian (SAS)

AF:

0.233

AC:

1125

AN:

4820

European-Finnish (FIN)

AF:

0.330

AC:

3484

AN:

10550

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.193

AC:

13089

AN:

67984

Other (OTH)

AF:

0.142

AC:

300

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1046

2092

3139

4185

5231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.114

Hom.:

240

Bravo

AF:

0.152

Asia WGS

AF:

0.245

AC:

850

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.56

(source)

DANN

Benign

0.29

PhyloP100

-0.69

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