16-90044871-G-T

Position:

• chr16-90044871-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001481.3(GAS8):​c.*1526G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 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 NM_001481.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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]

URAHP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GAS8	NM_001481.3	c.*1526G>T		3_prime_UTR_variant	11/11	ENST00000268699.9	NP_001472.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAS8	ENST00000268699.9	c.*1526G>T		3_prime_UTR_variant	11/11	1	NM_001481.3	ENSP00000268699.4

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56902 AN: 151948 Hom.: 12159 Cov.: 33

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.: 0 AF XY: 0.290 AC XY: 12853 AN XY: 44266

Gnomad4 AFR exome AF: 0.525

Gnomad4 AMR exome AF: 0.414

Gnomad4 ASJ exome AF: 0.207

Gnomad4 EAS exome AF: 0.648

Gnomad4 SAS exome AF: 0.314

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.233

Gnomad4 OTH exome AF: 0.297

GnomAD4 genome AF: 0.375 AC: 56996 AN: 152066 Hom.: 12194 Cov.: 33 AF XY: 0.383 AC XY: 28430 AN XY: 74322

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.320

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
DANN	Benign	0.58

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: rs8577; hg19: chr16-90111279;