NM_015472.6:c.672G>C

Variant names:

• chr3-149542434-C-G
• NM_015472.6:c.672G>C
• WWTR1 p.Ala224Ala

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_015472.6(WWTR1):​c.672G>C​(p.Ala224Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A224A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: WWTR1 NM_015472.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.51
• 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP7: Synonymous conserved (PhyloP=-5.51 with no splicing effect.

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.672G>C	p.Ala224Ala	synonymous	Exon 4 of 7	NP_056287.1	Q9GZV5
	WWTR1	NM_001168278.3		c.672G>C	p.Ala224Ala	synonymous	Exon 5 of 8	NP_001161750.1	Q9GZV5
	WWTR1	NM_001168280.3		c.672G>C	p.Ala224Ala	synonymous	Exon 4 of 7	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.672G>C	p.Ala224Ala	synonymous	Exon 4 of 7	ENSP00000353847.3	Q9GZV5
	WWTR1	ENST00000951296.1		c.535G>C	p.Ala179Pro	missense	Exon 3 of 7	ENSP00000621355.1
	WWTR1	ENST00000465804.5	TSL:2	c.672G>C	p.Ala224Ala	synonymous	Exon 5 of 8	ENSP00000419465.1	Q9GZV5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		-5.5

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

hg19: chr3-149260221;