Variant chr16-90022715-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001481.3(GAS8):c.-7T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00776 in 1,417,528 control chromosomes in the GnomAD database, including 555 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 329 hom., cov: 33)

Exomes 𝑓: 0.0043 ( 226 hom. )

Consequence

GAS8
NM_001481.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.338

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 16-90022715-T-G is Benign according to our data. Variant chr16-90022715-T-G is described in ClinVar as [Benign]. Clinvar id is 1236662.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS8	NM_001481.3 linkuse as main transcript	c.-7T>G		5_prime_UTR_variant	1/11	ENST00000268699.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS8	ENST00000268699.9 linkuse as main transcript	c.-7T>G		5_prime_UTR_variant	1/11	1	NM_001481.3	P4	O95995-1

Frequencies

GnomAD3 genomes

AF:

0.0366

AC:

5563

AN:

151912

Hom.:

329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0160

Gnomad ASJ

AF:

0.00289

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00498

Gnomad FIN

AF:

0.0000948

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00135

Gnomad OTH

AF:

0.0187

GnomAD3 exomes

AF:

0.00489

AC:

329

AN:

67332

Hom.:

AF XY:

0.00462

AC XY:

179

AN XY:

38758

show subpopulations

Gnomad AFR exome

AF:

0.0808

Gnomad AMR exome

AF:

0.00668

Gnomad ASJ exome

AF:

0.00219

Gnomad EAS exome

AF:

0.00181

Gnomad SAS exome

AF:

0.00515

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000950

Gnomad OTH exome

AF:

0.00444

GnomAD4 exome

AF:

0.00429

AC:

5432

AN:

1265500

Hom.:

226

Cov.:

AF XY:

0.00411

AC XY:

2542

AN XY:

618122

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.00833

Gnomad4 ASJ exome

AF:

0.00246

Gnomad4 EAS exome

AF:

0.000105

Gnomad4 SAS exome

AF:

0.00566

Gnomad4 FIN exome

AF:

0.000227

Gnomad4 NFE exome

AF:

0.00109

Gnomad4 OTH exome

AF:

0.00932

GnomAD4 genome

AF:

0.0366

AC:

5568

AN:

152028

Hom.:

329

Cov.:

AF XY:

0.0353

AC XY:

2622

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.0160

Gnomad4 ASJ

AF:

0.00289

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.00499

Gnomad4 FIN

AF:

0.0000948

Gnomad4 NFE

AF:

0.00135

Gnomad4 OTH

AF:

0.0185

Alfa

AF:

0.00181

Hom.:

Bravo

AF:

0.0401

Asia WGS

AF:

0.00982

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia 33

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 22, 2023

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.99

DANN

Benign

0.49

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over