rs1238487571

Variant names:

• chr16-67391006-C-A
• rs1238487571
• NM_015964.4:c.106G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-67391006-C-A
• chr16-67391006-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015964.4(TPPP3):​c.106G>T​(p.Ala36Ser) variant causes a missense 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. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A36T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TPPP3 NM_015964.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.60
• Publications: 2 publications found

Genes affected

TPPP3 (HGNC:24162): (tubulin polymerization promoting protein family member 3) Enables tubulin binding activity. Involved in decidualization and microtubule bundle formation. Colocalizes with microtubule bundle and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

RNU1-123P (HGNC:48465): (RNA, U1 small nuclear 123, pseudogene)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14709067).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015964.4. 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
	TPPP3	NM_015964.4	MANE Select	c.106G>T	p.Ala36Ser	missense	Exon 2 of 4	NP_057048.2	Q9BW30
	TPPP3	NM_016140.4		c.106G>T	p.Ala36Ser	missense	Exon 3 of 5	NP_057224.2	Q9BW30

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPPP3	ENST00000393957.7	TSL:1 MANE Select	c.106G>T	p.Ala36Ser	missense	Exon 2 of 4	ENSP00000377529.2	Q9BW30
	TPPP3	ENST00000564104.5	TSL:1	c.106G>T	p.Ala36Ser	missense	Exon 1 of 3	ENSP00000462435.1	Q9BW30
	TPPP3	ENST00000290942.9	TSL:2	c.106G>T	p.Ala36Ser	missense	Exon 3 of 5	ENSP00000290942.5	Q9BW30

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	21
DANN	Benign	0.88
DEOGEN2	Benign	0.017	T
Eigen	Benign	-0.39
Eigen_PC	Benign	-0.12
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.75	N
PhyloP100		2.6
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	0.17	N
REVEL	Benign	0.13
Sift	Benign	0.97	T
Sift4G	Benign	0.80	T
Polyphen		0.0	B
Vest4		0.32
MutPred		0.39		Gain of disorder (P = 0.03)
MVP		0.38
MPC		0.41
ClinPred		0.45	T
GERP RS		5.0
Varity_R		0.18
gMVP		0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1238487571; hg19: chr16-67424909;