Variant chr22-31956804-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003405.4(YWHAH):c.*12G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,565,662 control chromosomes in the GnomAD database, including 74,632 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 0.24 ( 5418 hom., cov: 32)

Exomes 𝑓: 0.31 ( 69214 hom. )

Consequence

YWHAH
NM_003405.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.601

Variant links:

Genes affected

YWHAH (HGNC:12853): (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta) 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 bovine orthologs. This gene contains a 7 bp repeat sequence in its 5' UTR, and changes in the number of this repeat have been associated with early-onset schizophrenia and psychotic bipolar disorder. [provided by RefSeq, Jun 2009]

YWHAH links:

YWHAH (HGNC:):

YWHAH links:

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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=-0.69).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YWHAH	NM_003405.4 linkuse as main transcript	c.*12G>A		3_prime_UTR_variant	2/2	ENST00000248975.6	NP_003396.1	Q04917A0A024R1K7Q9H4N8

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
YWHAH	ENST00000248975.6 linkuse as main transcript	c.*12G>A	3_prime_UTR_variant	2/2	1	NM_003405.4	ENSP00000248975.5	Q04917
YWHAH	ENST00000397492.1 linkuse as main transcript	c.*649G>A	3_prime_UTR_variant	3/3	3		ENSP00000380629.1	A2IDB1
YWHAH	ENST00000471374.1 linkuse as main transcript	n.936G>A	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36484

AN:

151980

Hom.:

5411

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0718

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.336

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.256

GnomAD3 exomes

AF:

0.291

AC:

53306

AN:

183110

Hom.:

8120

AF XY:

0.296

AC XY:

28757

AN XY:

97304

show subpopulations

Gnomad AFR exome

AF:

0.0690

Gnomad AMR exome

AF:

0.349

Gnomad ASJ exome

AF:

0.339

Gnomad EAS exome

AF:

0.154

Gnomad SAS exome

AF:

0.290

Gnomad FIN exome

AF:

0.294

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.305

GnomAD4 exome

AF:

0.308

AC:

434890

AN:

1413564

Hom.:

69214

Cov.:

AF XY:

0.307

AC XY:

214767

AN XY:

698720

show subpopulations

Gnomad4 AFR exome

AF:

0.0635

Gnomad4 AMR exome

AF:

0.334

Gnomad4 ASJ exome

AF:

0.326

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.323

Gnomad4 OTH exome

AF:

0.294

GnomAD4 genome

AF:

0.240

AC:

36503

AN:

152098

Hom.:

5418

Cov.:

AF XY:

0.242

AC XY:

18002

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0718

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.336

Gnomad4 EAS

AF:

0.142

Gnomad4 SAS

AF:

0.284

Gnomad4 FIN

AF:

0.299

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.258

Alfa

AF:

0.236

Hom.:

1261

Bravo

AF:

0.230

Asia WGS

AF:

0.220

AC:

763

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over