3-149601710-ATTTTT-ATTTTTT

Position:

• chr3-149601710-ATTTTT-ATTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015472.6(WWTR1):​c.432-28711dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.063 (673 hom., cov: 0)
• Consequence: WWTR1 NM_015472.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

Genes affected

WWTR1 (HGNC:24042): (WW domain containing transcription regulator 1) Enables transcription coactivator activity. Involved in several processes, including hippo signaling; positive regulation of cell differentiation; and regulation of signal transduction. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WWTR1	NM_015472.6	c.432-28711dupA		intron_variant		ENST00000360632.8	NP_056287.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WWTR1	ENST00000360632.8	c.432-28711dupA		intron_variant		1	NM_015472.6	ENSP00000353847.3
WWTR1	ENST00000465804.5	c.432-28711dupA		intron_variant		2		ENSP00000419465.1
WWTR1	ENST00000467467.5	c.432-28711dupA		intron_variant		5		ENSP00000419234.1
WWTR1	ENST00000479238.1	c.432-28711dupA		intron_variant		3		ENSP00000418580.1

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9515 AN: 150594 Hom.: 671 Cov.: 0

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00617

Gnomad OTH AF: 0.0558

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

GnomAD4 genome AF: 0.0633 AC: 9533 AN: 150708 Hom.: 673 Cov.: 0 AF XY: 0.0652 AC XY: 4804 AN XY: 73640

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.0212

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.00617

Gnomad4 OTH AF: 0.0557

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3976504; hg19: chr3-149319497;