rs7830371

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLVS1	XM_017013141.2	c.-152+11248G>T		intron_variant	Intron 2 of 6		XP_016868630.1
CLVS1	XM_024447079.2	c.-289+11248G>T		intron_variant	Intron 3 of 8		XP_024302847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLVS1	ENST00000522621.1	c.-152+11248G>T		intron_variant	Intron 2 of 2	4		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 v4.3

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;