rs1486649

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-61235436-A-C
• chr8-61235436-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLVS1	XM_017013141.2	c.-151-64241A>C		intron_variant	Intron 2 of 6		XP_016868630.1
CLVS1	XM_024447079.2	c.-288-56882A>C		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.-151-64241A>C		intron_variant	Intron 2 of 2	4		ENSP00000428986.1
ENSG00000254222	ENST00000719681.1	n.296-1934T>G		intron_variant	Intron 2 of 2
ENSG00000254222	ENST00000719682.1	n.351+1887T>G		intron_variant	Intron 3 of 3

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 v4.3

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;