rs983583

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77
Variant links:
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]

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ACMG classification

Classification made for transcript

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
YWHAZNM_145690.3 linkuse as main transcriptc.-11-782A>G intron_variant ENST00000395958.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
YWHAZENST00000395958.6 linkuse as main transcriptc.-11-782A>G intron_variant 1 NM_145690.3 P1P63104-1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs983583; hg19: chr8-101961910; API