Genetic Variant GAS8:n.*2923G>T (chr16-90044871-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000566266.5(GAS8):n.*2923G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 234,702 control chromosomes in the GnomAD database, including 16,302 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 0.37 ( 12194 hom., cov: 33)

Exomes 𝑓: 0.29 ( 4108 hom. )

Consequence

GAS8
ENST00000566266.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Publications

9 publications found

Variant links:

Genes affected

GAS8 (HGNC:4166): (growth arrest specific 8) This gene includes 11 exons spanning 25 kb and maps to a region of chromosome 16 that is sometimes deleted in breast and prostrate cancer. The second intron contains an apparently intronless gene, C16orf3, that is transcribed in the opposite orientation. This gene is a putative tumor suppressor gene. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

GAS8 links:

URAHP (HGNC:):

URAHP links:

URAHP (HGNC:43695): (urate (hydroxyiso-) hydrolase, pseudogene) Predicted to enable hydroxyisourate hydrolase activity. Predicted to be involved in allantoin metabolic process; purine-containing compound catabolic process; and urate catabolic process. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

URAHP 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRC4	NM_001481.3 link	c.*1526G>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000268699.9	NP_001472.1	O95995-1A0A384MR00

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS8	ENST00000268699.9 link	c.*1526G>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_001481.3	ENSP00000268699.4		O95995-1

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56902

AN:

151948

Hom.:

12159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.555

Gnomad AMI

AF:

0.187

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.322

GnomAD4 exome

AF:

0.288

AC:

23795

AN:

82636

Hom.:

4108

Cov.:

AF XY:

0.290

AC XY:

12853

AN XY:

44266

show subpopulations

African (AFR)

AF:

0.525

AC:

915

AN:

1742

American (AMR)

AF:

0.414

AC:

1675

AN:

4044

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

371

AN:

1792

East Asian (EAS)

AF:

0.648

AC:

1923

AN:

2968

South Asian (SAS)

AF:

0.314

AC:

4797

AN:

15270

European-Finnish (FIN)

AF:

0.385

AC:

1493

AN:

3882

Middle Eastern (MID)

AF:

0.259

AC:

AN:

348

European-Non Finnish (NFE)

AF:

0.233

AC:

11251

AN:

48278

Other (OTH)

AF:

0.297

AC:

1280

AN:

4312

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

733

1467

2200

2934

3667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

280

420

560

700

<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:

0.375

AC:

56996

AN:

152066

Hom.:

12194

Cov.:

AF XY:

0.383

AC XY:

28430

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.555

AC:

23009

AN:

41450

American (AMR)

AF:

0.397

AC:

6075

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

796

AN:

3464

East Asian (EAS)

AF:

0.632

AC:

3268

AN:

5168

South Asian (SAS)

AF:

0.351

AC:

1692

AN:

4818

European-Finnish (FIN)

AF:

0.421

AC:

4447

AN:

10572

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.247

AC:

16804

AN:

67980

Other (OTH)

AF:

0.320

AC:

677

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1693

3386

5080

6773

8466

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.293

Hom.:

1498

Bravo

AF:

0.384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.086

(source)

DANN

Benign

0.58

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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