Variant 16-90043348-GC-GCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001481.3(GAS8):c.*9dupC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,602,956 control chromosomes in the GnomAD database, including 81,720 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 13560 hom., cov: 0)

Exomes 𝑓: 0.29 ( 68160 hom. )

Consequence

GAS8
NM_001481.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.863

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-90043348-G-GC is Benign according to our data. Variant chr16-90043348-G-GC is described in ClinVar as [Benign]. Clinvar id is 402895.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAS8	NM_001481.3 linkuse as main transcript	c.*9dupC		3_prime_UTR_variant	11/11	ENST00000268699.9	NP_001472.1	O95995-1A0A384MR00

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAS8	ENST00000268699.9 linkuse as main transcript	c.*9dupC		3_prime_UTR_variant	11/11	1	NM_001481.3	ENSP00000268699.4		O95995-1

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59391

AN:

152002

Hom.:

13522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.604

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.637

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.332

GnomAD3 exomes

AF:

0.365

AC:

87090

AN:

238882

Hom.:

18231

AF XY:

0.352

AC XY:

45895

AN XY:

130388

show subpopulations

Gnomad AFR exome

AF:

0.609

Gnomad AMR exome

AF:

0.472

Gnomad ASJ exome

AF:

0.236

Gnomad EAS exome

AF:

0.643

Gnomad SAS exome

AF:

0.366

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.316

GnomAD4 exome

AF:

0.288

AC:

417778

AN:

1450840

Hom.:

68160

Cov.:

AF XY:

0.288

AC XY:

207481

AN XY:

720886

show subpopulations

Gnomad4 AFR exome

AF:

0.618

Gnomad4 AMR exome

AF:

0.466

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.677

Gnomad4 SAS exome

AF:

0.367

Gnomad4 FIN exome

AF:

0.409

Gnomad4 NFE exome

AF:

0.246

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.391

AC:

59480

AN:

152116

Hom.:

13560

Cov.:

AF XY:

0.399

AC XY:

29682

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.604

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.637

Gnomad4 SAS

AF:

0.371

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.249

Gnomad4 OTH

AF:

0.330

Bravo

AF:

0.400

Asia WGS

AF:

0.499

AC:

1740

AN:

3478

EpiCase

AF:

0.236

EpiControl

AF:

0.241

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Primary ciliary dyskinesia 33

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 17, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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