rs10857809

Variant names:

• chr1-110052906-C-A
• rs10857809
• NM_033088.4:c.2267-759C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-110052906-C-A
• chr1-110052906-C-G
• chr1-110052906-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033088.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP1	NM_033088.4	MANE Select	c.2267-759C>A		intron	N/A	NP_149079.2
	STRIP1	NM_001270768.2		c.1982-759C>A		intron	N/A	NP_001257697.1
	STRIP1	NR_073071.2		n.2395-759C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP1	ENST00000369795.8	TSL:1 MANE Select	c.2267-759C>A		intron	N/A	ENSP00000358810.3
	STRIP1	ENST00000485775.5	TSL:1	n.*1742-759C>A		intron	N/A	ENSP00000476025.1
	STRIP1	ENST00000369796.5	TSL:2	c.1982-759C>A		intron	N/A	ENSP00000358811.1

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

African (AFR) AF: 0.222 AC: 9223 AN: 41500

American (AMR) AF: 0.306 AC: 4678 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1943 AN: 5170

South Asian (SAS) AF: 0.470 AC: 2265 AN: 4820

European-Finnish (FIN) AF: 0.189 AC: 2002 AN: 10616

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14698 AN: 67978

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.215 Hom.: 4714

Bravo AF: 0.244

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.76
PhyloP100		-0.34
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

Other links and lift over

dbSNP: rs10857809; hg19: chr1-110595528;