chr8-61141904-C-A

Variant names:

• chr8-61141904-C-A
• rs12681792
• ENST00000522621.1:c.-152+10044C>A

Variant summary

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

The ENST00000522621.1(CLVS1):​c.-152+10044C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,060 control chromosomes in the GnomAD database, including 4,479 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 0.23 (4479 hom., cov: 32)
• Consequence: CLVS1 ENST00000522621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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.-152+10044C>A		intron	N/A	ENSP00000428986.1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35224 AN: 151942 Hom.: 4474 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.232 AC: 35243 AN: 152060 Hom.: 4479 Cov.: 32 AF XY: 0.236 AC XY: 17555 AN XY: 74320

African (AFR) AF: 0.304 AC: 12596 AN: 41462

American (AMR) AF: 0.137 AC: 2089 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1513 AN: 5176

South Asian (SAS) AF: 0.231 AC: 1110 AN: 4810

European-Finnish (FIN) AF: 0.331 AC: 3492 AN: 10554

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13380 AN: 67990

Other (OTH) AF: 0.188 AC: 397 AN: 2116

Alfa AF: 0.203 Hom.: 1129

Bravo AF: 0.220

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs12681792; hg19: chr8-62054463;