rs983583

Positions:

• chr8-100949682-T-C

Variant summary

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

The NM_145690.3(YWHAZ):​c.-11-782A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,062 control chromosomes in the GnomAD database, including 33,265 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 0.66 (33265 hom., cov: 32)
• Consequence: YWHAZ NM_145690.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

YWHAZ (HGNC:12855): (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta) This gene product belongs to the 14-3-3 family of proteins which mediate signal transduction by binding to phosphoserine-containing proteins. This highly conserved protein family is found in both plants and mammals, and this protein is 99% identical to the mouse, rat and sheep orthologs. The encoded protein interacts with IRS1 protein, suggesting a role in regulating insulin sensitivity. Several transcript variants that differ in the 5' UTR but that encode the same protein have been identified for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YWHAZ	NM_145690.3	c.-11-782A>G		intron_variant		ENST00000395958.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YWHAZ	ENST00000395958.6	c.-11-782A>G		intron_variant		1	NM_145690.3	P1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99683 AN: 151944 Hom.: 33234 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.656 AC: 99757 AN: 152062 Hom.: 33265 Cov.: 32 AF XY: 0.652 AC XY: 48462 AN XY: 74342

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.642

Alfa AF: 0.631 Hom.: 13847

Bravo AF: 0.670

Asia WGS AF: 0.646 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.65

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: rs983583; hg19: chr8-101961910;