8-61143108-G-T

Variant names:

• chr8-61143108-G-T
• rs7830371
• ENST00000522621.1:c.-152+11248G>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+11248G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 152,102 control chromosomes in the GnomAD database, including 17,680 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 0.46 (17680 hom., cov: 33)
• Consequence: CLVS1 ENST00000522621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 5 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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLVS1	ENST00000522621.1	TSL:4	c.-152+11248G>T		intron	N/A	ENSP00000428986.1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69692 AN: 151984 Hom.: 17688 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.458 AC: 69699 AN: 152102 Hom.: 17680 Cov.: 33 AF XY: 0.445 AC XY: 33058 AN XY: 74348

African (AFR) AF: 0.318 AC: 13202 AN: 41476

American (AMR) AF: 0.411 AC: 6282 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2266 AN: 3470

East Asian (EAS) AF: 0.0382 AC: 198 AN: 5184

South Asian (SAS) AF: 0.317 AC: 1530 AN: 4826

European-Finnish (FIN) AF: 0.451 AC: 4763 AN: 10562

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39800 AN: 67988

Other (OTH) AF: 0.479 AC: 1011 AN: 2112

Alfa AF: 0.537 Hom.: 62686

Bravo AF: 0.446

Asia WGS AF: 0.191 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.7
DANN	Benign	0.84
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs7830371; hg19: chr8-62055667;