1-110052906-C-A

Position:

• chr1-110052906-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033088.4(STRIP1):​c.2267-759C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,160 control chromosomes in the GnomAD database, including 4,615 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4615 hom., cov: 32)
• Consequence: STRIP1 NM_033088.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

STRIP1 (HGNC:25916): (striatin interacting protein 1) This gene encodes a member of the striatin-interacting phosphatase and kinase complex, which is involved in localization of the Golgi body. The encoded protein participates in cytosketelal organization. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

STRIP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRIP1	NM_033088.4	c.2267-759C>A		intron_variant		ENST00000369795.8	NP_149079.2
STRIP1	NM_001270768.2	c.1982-759C>A		intron_variant			NP_001257697.1
STRIP1	XM_006710995.3	c.1349-759C>A		intron_variant			XP_006711058.1
STRIP1	NR_073071.2	n.2395-759C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRIP1	ENST00000369795.8	c.2267-759C>A		intron_variant		1	NM_033088.4	ENSP00000358810.3
STRIP1	ENST00000485775.5	n.*1742-759C>A		intron_variant		1		ENSP00000476025.1
STRIP1	ENST00000369796.5	c.1982-759C>A		intron_variant		2		ENSP00000358811.1
STRIP1	ENST00000473429.5	n.3076-759C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36366 AN: 152042 Hom.: 4608 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.239 AC: 36399 AN: 152160 Hom.: 4615 Cov.: 32 AF XY: 0.243 AC XY: 18086 AN XY: 74404

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.241

Alfa AF: 0.209 Hom.: 3358

Bravo AF: 0.244

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.76

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: rs10857809; hg19: chr1-110595528;