rs11544766

Variant names:

• chr11-6320274-C-G
• rs11544766
• NM_145040.3:c.203G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-6320274-C-G
• chr11-6320274-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_145040.3(CAVIN3):​c.203G>C​(p.Ser68Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000517 in 1,565,872 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0027 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00028 (1 hom.)
• Consequence: CAVIN3 NM_145040.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.868
• Publications: 2 publications found

Genes affected

CAVIN3 (HGNC:9400): (caveolae associated protein 3) The protein encoded by this gene was identified as a binding protein of the protein kinase C, delta (PRKCD). The expression of this gene in cultured cell lines is strongly induced by serum starvation. The expression of this protein was found to be down-regulated in various cancer cell lines, suggesting the possible tumor suppressor function of this protein. [provided by RefSeq, Jul 2008]

ENSG00000282556 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.008076578).
• BS2: High AC in GnomAd4 at 413 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145040.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAVIN3	NM_145040.3	MANE Select	c.203G>C	p.Ser68Thr	missense	Exon 1 of 2	NP_659477.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAVIN3	ENST00000303927.4	TSL:1 MANE Select	c.203G>C	p.Ser68Thr	missense	Exon 1 of 2	ENSP00000307292.3	Q969G5
	CAVIN3	ENST00000530979.1	TSL:2	c.203G>C	p.Ser68Thr	missense	Exon 1 of 3	ENSP00000432047.1	E9PIE3
	CAVIN3	ENST00000954671.1		c.203G>C	p.Ser68Thr	missense	Exon 1 of 3	ENSP00000624730.1

Frequencies

GnomAD3 genomes AF: 0.00271 AC: 413 AN: 152228 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00938

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00191

GnomAD2 exomes AF: 0.000597 AC: 101 AN: 169206 AF XY: 0.000552

Gnomad AFR exome AF: 0.00968

Gnomad AMR exome AF: 0.000280

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000140

Gnomad OTH exome AF: 0.000645

GnomAD4 exome AF: 0.000280 AC: 396 AN: 1413526 Hom.: 1 Cov.: 33 AF XY: 0.000245 AC XY: 172 AN XY: 700960

African (AFR) AF: 0.0102 AC: 332 AN: 32480

American (AMR) AF: 0.000200 AC: 8 AN: 39912

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25480

East Asian (EAS) AF: 0.00 AC: 0 AN: 37472

South Asian (SAS) AF: 0.0000365 AC: 3 AN: 82206

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36342

Middle Eastern (MID) AF: 0.000529 AC: 3 AN: 5674

European-Non Finnish (NFE) AF: 0.00000548 AC: 6 AN: 1095066

Other (OTH) AF: 0.000747 AC: 44 AN: 58894

GnomAD4 genome AF: 0.00271 AC: 413 AN: 152346 Hom.: 0 Cov.: 33 AF XY: 0.00246 AC XY: 183 AN XY: 74498

African (AFR) AF: 0.00938 AC: 390 AN: 41592

American (AMR) AF: 0.00105 AC: 16 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68024

Other (OTH) AF: 0.00189 AC: 4 AN: 2114

Alfa AF: 0.000557 Hom.: 1

Bravo AF: 0.00318

ESP6500AA AF: 0.00707 AC: 30

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000523 AC: 61

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.33
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.079	T
Eigen	Uncertain	0.27
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Benign	0.088	N
LIST_S2	Benign	0.68	T
MetaRNN	Benign	0.0081	T
MetaSVM	Benign	-0.71	T
PhyloP100		0.87
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.091
Sift	Benign	0.17	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.93	P
Vest4		0.068
MVP		0.55
MPC		1.1
ClinPred		0.036	T
GERP RS		4.9
PromoterAI		0.036	Neutral
Varity_R		0.28
gMVP		0.28
Mutation Taster		=93/7	polymorphism

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

Other links and lift over

dbSNP: rs11544766; hg19: chr11-6341504;