7-129434483-C-T

Variant names:

• chr7-129434483-C-T
• rs1348518896
• NM_020704.3:c.11C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_020704.3(STRIP2):​c.11C>T​(p.Pro4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000132 in 1,514,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P4S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: STRIP2 NM_020704.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.242
• Publications: 1 publications found

Genes affected

STRIP2 (HGNC:22209): (striatin interacting protein 2) Involved in cell migration; cytoskeleton organization; and regulation of cell shape. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

STRIP2 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000300026 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.036278635).
• BP6: Variant 7-129434483-C-T is Benign according to our data. Variant chr7-129434483-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3802674.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020704.3. 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
	STRIP2	NM_020704.3	MANE Select	c.11C>T	p.Pro4Leu	missense	Exon 1 of 21	NP_065755.1	Q9ULQ0-1
	STRIP2	NM_001134336.2		c.11C>T	p.Pro4Leu	missense	Exon 1 of 20	NP_001127808.1	Q9ULQ0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP2	ENST00000249344.7	TSL:1 MANE Select	c.11C>T	p.Pro4Leu	missense	Exon 1 of 21	ENSP00000249344.2	Q9ULQ0-1
	STRIP2	ENST00000435494.2	TSL:1	c.11C>T	p.Pro4Leu	missense	Exon 1 of 20	ENSP00000392393.2	Q9ULQ0-2
	STRIP2	ENST00000947594.1		c.11C>T	p.Pro4Leu	missense	Exon 1 of 21	ENSP00000617653.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152232 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 7.34e-7 AC: 1 AN: 1362268 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 671036

African (AFR) AF: 0.00 AC: 0 AN: 28720

American (AMR) AF: 0.00 AC: 0 AN: 34400

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24420

East Asian (EAS) AF: 0.00 AC: 0 AN: 33488

South Asian (SAS) AF: 0.00 AC: 0 AN: 76894

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33356

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4030

European-Non Finnish (NFE) AF: 9.34e-7 AC: 1 AN: 1070102

Other (OTH) AF: 0.00 AC: 0 AN: 56858

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152232 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74370

African (AFR) AF: 0.00 AC: 0 AN: 41464

American (AMR) AF: 0.0000654 AC: 1 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4836

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68036

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.95
DEOGEN2	Benign	0.0074	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.052	N
LIST_S2	Benign	0.66	T
M_CAP	Benign	0.074	D
MetaRNN	Benign	0.036	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.24
PrimateAI	Uncertain	0.62	T
PROVEAN	Benign	-0.56	N
REVEL	Benign	0.033
Sift	Benign	0.77	T
Sift4G	Uncertain	0.021	D
Polyphen		0.0	B
Vest4		0.049
MutPred		0.11		Loss of relative solvent accessibility (P = 0.0306)
MVP		0.072
MPC		0.22
ClinPred		0.25	T
GERP RS		2.7
PromoterAI		0.14	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1
Varity_R		0.034
gMVP		0.18
Mutation Taster		=97/3	polymorphism

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

Other links and lift over

dbSNP: rs1348518896; hg19: chr7-129074324;