16-90023055-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001481.3(GAS8):c.3+331C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,052 control chromosomes in the GnomAD database, including 7,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (7805 hom., cov: 32)
• Consequence: GAS8 NM_001481.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.02

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 16-90023055-C-G is Benign according to our data. Variant chr16-90023055-C-G is described in ClinVar as [Benign]. Clinvar id is 1222931.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS8	NM_001481.3	c.3+331C>G		intron_variant		ENST00000268699.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS8	ENST00000268699.9	c.3+331C>G		intron_variant		1	NM_001481.3	P4

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48209 AN: 151932 Hom.: 7791 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.317 AC: 48254 AN: 152052 Hom.: 7805 Cov.: 32 AF XY: 0.317 AC XY: 23559 AN XY: 74328

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.341

Alfa AF: 0.316 Hom.: 951

Bravo AF: 0.315

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 31, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.70
Dann	Benign	0.79

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

Other links and lift over

dbSNP: rs870856; hg19: chr16-90089463;