ENST00000554749.1:n.836C>G

Variant names:

• chr1-110059175-C-G
• rs10857810
• ENST00000554749.1:n.836C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554749.1(ENSG00000258634):​n.836C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,174 control chromosomes in the GnomAD database, including 3,874 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 0.21 (3874 hom., cov: 32)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: ENSG00000258634 ENST00000554749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 2 publications found

Genes affected

ENSG00000258634 (HGNC:):

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=-0.77).
• 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: ENST00000554749.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258634	ENST00000554749.1	TSL:6	n.836C>G		non_coding_transcript_exon	Exon 1 of 1
	STRIP1	ENST00000473429.5	TSL:2	n.4213+4373C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32058 AN: 151994 Hom.: 3870 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.145 AC: 9 AN: 62 Hom.: 0 Cov.: 0 AF XY: 0.146 AC XY: 7 AN XY: 48

African (AFR) AF: 0.375 AC: 3 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0833 AC: 4 AN: 48

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.211 AC: 32084 AN: 152112 Hom.: 3874 Cov.: 32 AF XY: 0.216 AC XY: 16057 AN XY: 74354

African (AFR) AF: 0.119 AC: 4930 AN: 41508

American (AMR) AF: 0.297 AC: 4535 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1946 AN: 5144

South Asian (SAS) AF: 0.470 AC: 2264 AN: 4818

European-Finnish (FIN) AF: 0.199 AC: 2101 AN: 10584

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14783 AN: 67986

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.211 Hom.: 481

Bravo AF: 0.211

Asia WGS AF: 0.394 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs10857810; hg19: chr1-110601797; COSMIC: COSV63928644;