3-149601710-ATTTTT-ATTTT

Variant names:

• chr3-149601710-AT-A
• rs3976504
• NM_015472.6:c.432-28711delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015472.6(WWTR1):​c.432-28711delA 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 0.71 (38028 hom., cov: 0)
• Consequence: WWTR1 NM_015472.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015472.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WWTR1	NM_015472.6	MANE Select	c.432-28711delA		intron	N/A	NP_056287.1	Q9GZV5
	WWTR1	NM_001168278.3		c.432-28711delA		intron	N/A	NP_001161750.1	Q9GZV5
	WWTR1	NM_001168280.3		c.432-28711delA		intron	N/A	NP_001161752.1	Q9GZV5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WWTR1	ENST00000360632.8	TSL:1 MANE Select	c.432-28711delA		intron	N/A	ENSP00000353847.3	Q9GZV5
	WWTR1	ENST00000465804.5	TSL:2	c.432-28711delA		intron	N/A	ENSP00000419465.1	Q9GZV5
	WWTR1	ENST00000467467.5	TSL:5	c.432-28711delA		intron	N/A	ENSP00000419234.1	Q9GZV5

Frequencies

GnomAD3 genomes AF: 0.709 AC: 106756 AN: 150566 Hom.: 37998 Cov.: 0

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.709 AC: 106841 AN: 150680 Hom.: 38028 Cov.: 0 AF XY: 0.708 AC XY: 52134 AN XY: 73612

African (AFR) AF: 0.626 AC: 25734 AN: 41128

American (AMR) AF: 0.711 AC: 10788 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2519 AN: 3460

East Asian (EAS) AF: 0.674 AC: 3479 AN: 5160

South Asian (SAS) AF: 0.833 AC: 3965 AN: 4760

European-Finnish (FIN) AF: 0.734 AC: 7419 AN: 10110

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50485 AN: 67580

Other (OTH) AF: 0.690 AC: 1449 AN: 2100

Alfa AF: 0.674 Hom.: 1335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3976504; hg19: chr3-149319497;