ENST00000522621.1:c.-151-64241A>C

Variant names:

• chr8-61235436-A-C
• rs1486649
• ENST00000522621.1:c.-151-64241A>C

Variant summary

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

The ENST00000522621.1(CLVS1):​c.-151-64241A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,226 control chromosomes in the GnomAD database, including 3,601 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 0.16 (3601 hom., cov: 33)
• Consequence: CLVS1 ENST00000522621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 1 publications found

Genes affected

CLVS1 (HGNC:23139): (clavesin 1) Enables phosphatidylinositol-3,5-bisphosphate binding activity. Predicted to be involved in lysosome organization. Located in endosome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254222 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522621.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLVS1	ENST00000522621.1	TSL:4	c.-151-64241A>C		intron	N/A	ENSP00000428986.1
	ENSG00000254222	ENST00000719681.1		n.296-1934T>G		intron	N/A
	ENSG00000254222	ENST00000719682.1		n.351+1887T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24291 AN: 152108 Hom.: 3594 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.160 AC: 24327 AN: 152226 Hom.: 3601 Cov.: 33 AF XY: 0.168 AC XY: 12539 AN XY: 74436

African (AFR) AF: 0.280 AC: 11641 AN: 41510

American (AMR) AF: 0.182 AC: 2777 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3539 AN: 5172

South Asian (SAS) AF: 0.326 AC: 1574 AN: 4822

European-Finnish (FIN) AF: 0.0755 AC: 801 AN: 10612

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3244 AN: 68036

Other (OTH) AF: 0.148 AC: 312 AN: 2106

Alfa AF: 0.128 Hom.: 312

Bravo AF: 0.173

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.85
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1486649; hg19: chr8-62147995;