Genetic Variant CLVS1:c.977+159C>A (chr8-61458701-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_173519.3(CLVS1):c.977+159C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CLVS1
NM_173519.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.192

Publications

3 publications found

Variant links:

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]

CLVS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CLVS1	NM_173519.3 link	c.977+159C>A	intron_variant	Intron 5 of 5	ENST00000325897.5	NP_775790.1
CLVS1	XM_017013141.2 link	c.977+159C>A	intron_variant	Intron 6 of 6		XP_016868630.1	Q8IUQ0-1
CLVS1	XM_017013142.3 link	c.977+159C>A	intron_variant	Intron 6 of 6		XP_016868631.1	Q8IUQ0-1
CLVS1	XM_024447079.2 link	c.977+159C>A	intron_variant	Intron 8 of 8		XP_024302847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLVS1	ENST00000325897.5 link	c.977+159C>A		intron_variant	Intron 5 of 5	1	NM_173519.3	ENSP00000325506.4		Q8IUQ0-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

424156

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

221290

African (AFR)

AF:

0.00

AC:

AN:

11884

American (AMR)

AF:

0.00

AC:

AN:

12958

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12952

East Asian (EAS)

AF:

0.00

AC:

AN:

28946

South Asian (SAS)

AF:

0.00

AC:

AN:

35352

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30648

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3046

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

263942

Other (OTH)

AF:

0.00

AC:

AN:

24428

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

132451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over