rs17763714

Variant names:

• chr8-61138184-G-C
• rs17763714
• ENST00000522621.1:c.-152+6324G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-61138184-G-C
• chr8-61138184-G-T

Variant summary

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

The ENST00000522621.1(CLVS1):​c.-152+6324G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,146 control chromosomes in the GnomAD database, including 4,042 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 0.22 (4042 hom., cov: 32)
• Consequence: CLVS1 ENST00000522621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLVS1	ENST00000522621.1	TSL:4	c.-152+6324G>C		intron	N/A	ENSP00000428986.1	E5RK22

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33894 AN: 152028 Hom.: 4033 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.223 AC: 33933 AN: 152146 Hom.: 4042 Cov.: 32 AF XY: 0.224 AC XY: 16661 AN XY: 74374

African (AFR) AF: 0.170 AC: 7044 AN: 41494

American (AMR) AF: 0.332 AC: 5077 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 835 AN: 3472

East Asian (EAS) AF: 0.145 AC: 754 AN: 5186

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4816

European-Finnish (FIN) AF: 0.188 AC: 1993 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16089 AN: 67996

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.221 Hom.: 461

Bravo AF: 0.234

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.71
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs17763714; hg19: chr8-62050743;